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• 1000 Genomes Project Pilot 1 SNP Calling
  == (1) Create GLF files from BAM files == /home5/2009.08.GLF-1/
  7 KB (1,088 words) - 13:35, 10 March 2010

Page text matches

• 830 - MarkovModel::WalkLeft()
  matrix[0][i] = 1.; for (int i = 0; i < markers - 1; i++)
  654 bytes (81 words) - 09:24, 19 January 2017
• 830 - Haplotyper::RandomSetup()
  // i ranges from 0 .. individuals - 1 // j ranges from 0 .. markers - 1
  2 KB (162 words) - 15:56, 13 September 2013
• 830 - Haplotyper::SampleChromosomes()
  RetrieveMemoryBlock(markers - 1); SampleHaplotypes(leftMatrices[markers - 1], first, second, rand);
  1 KB (131 words) - 14:11, 2 October 2013
• 830 - Haplotyper::SummarizeOptions()
  right[0][0] = (1. - theta) * (1. - theta); right[1][0] = right[0][1] = (1. - theta) * theta / states;
  1 KB (110 words) - 15:55, 2 October 2013
• MaCH: Pedigree with Integer Allele Codes
  ...gree files, MaCH can accept pedigree files that encode bases A, C, G, T as 1, 2, 3, 4. Here is an example: FAM1001 ID1234 0 0 M 1 1 1 2 2 2
  649 bytes (96 words) - 10:24, 4 June 2010
• 830 - Haplotyper::ImputeGenotypes()
  RetrieveMemoryBlock(markers - 1); ImputeGenotypes(leftMatrices[markers - 1], markers - 1);
  722 bytes (69 words) - 14:19, 2 October 2013
• RAREFY TUTORIAL
  1994 5 1 2 1 4.05563 0.839037 2.73226 345 1 0 0 1 3.45514 0.785963 1.95526
  2 KB (193 words) - 05:10, 17 February 2015
• 830 - BestAlignment::IterateCache()
  while (cache[h] != -1 && cache[h] != key) h = h + 1 >= cacheSize ? 0 : h + 1;
  268 bytes (29 words) - 13:58, 28 October 2013
• 830 - Haplotyper::SampleOneHaplotype()
  return (first * (first + 1) / 2 + second); return (second * (second + 1) / 2 + first);
  513 bytes (50 words) - 16:03, 2 October 2013
• BamUtil: dumpRefInfo
  Ref ID: 0 Ref Name: 1 NumRecs: 4 Ref ID: -1 indicates unmapped (Ref Name will be *)
  2 KB (271 words) - 17:54, 6 January 2014
• BamUtil: dumpAsp
  ...cles for this position. There are numBases cycles, separated by a ':'. (-1 represents the cycle of a deletion) ...sition. Sequence of numBases 0's and 1's. 0 represents forward strand and 1 represents reverse strand.
  5 KB (646 words) - 17:39, 3 January 2014
• 830 - MaqIndex::GetWord()
  return -1; if (mask[i] == '1')
  500 bytes (64 words) - 13:39, 28 October 2013
• GotCloud: Filters
  {|border="1" cellspacing="0" cellpadding="2" ...Depth at Site || INFO:DP < #samples * FILTER_MIN_SAMPLE_DP > 0 || #samples*1
  4 KB (641 words) - 10:53, 29 October 2014
• Vcf2geno
  X5 X5 0 -9 0 0 0 2 2 1 2 2 2 1 10 1:10 A T
  3 KB (398 words) - 17:01, 19 February 2013
• 830 - MaqIndex::LookupWord()
  lastOccurrence = sortedPositions.Length() - 1; firstMax = probe - 1;
  1 KB (90 words) - 16:09, 28 October 2013
• FastQ Validation Criteria
  {| class="wikitable" style="width:100%" border="1" | Line is at least 2 characters long ('@' and at least 1 for the sequence identifier)
  3 KB (529 words) - 14:01, 7 September 2011
• Genotype Likelihood based Inbreeding Coefficient
  ...ue implies an excess of homozygotes. <math>F_{IC}</math> ranges from -1 to 1. F_{IC} & = 1 - \frac{O[Het]}{E[Het|\textbf{p}]} \\
  2 KB (404 words) - 15:53, 3 August 2015
• NHLBI Exome Sequencing Project
  * Phase 1 LungGO - ccds_2008 * Phase 1 WHISPGO - BMI/T2D - ccds_2008
  918 bytes (134 words) - 21:44, 14 September 2010
• BamUtil: gapInfo
  ...art of the 2nd read. (mate0BasedClippedStart - 0BasedPositionClippedEnd - 1) * chromosome is unknown (-1/*)
  5 KB (728 words) - 01:45, 6 March 2016
• 830 - MarkovModel::Impute()
  double ptotal = P[1] + P[2] + P[3] + P[4]; int mle = 1;
  1 KB (165 words) - 14:50, 25 September 2013
• ExomePicks
  1 I1 0 0 1 2 1 1 I2 0 0 2 2 1
  7 KB (964 words) - 10:01, 2 February 2017
• BamUtil: dumpIndex
  --summary : only print a summary - 1 line per reference. {{BamIndex|required=1}}
  1 KB (177 words) - 18:01, 6 January 2014
• RareSimu
  1. Heterogeneity Model 1. Heterogeneity Model
  2 KB (365 words) - 11:11, 2 February 2017
• Genotype Likelihood based Allele Frequency
  ...k}|G_{i,j})P(G_{i,j})^{(l-1)}}{\sum_{(i,j)}{P(R_{k}|G_{i,j})P(G_{i,j})^{(l-1)}}} ...th> and <math>j</math>. <math>k</math> indexes the individuals from <math>1</math> to <math>N</math>.
  3 KB (470 words) - 15:54, 3 August 2015
• BamUtil: indelDiscordance
  ** A base repeated once has repeat count = 1 ('AA') ...Deletion Discordance if at least 1 read has a match/mismatch AND at least 1 read has a deletion AND there are at least the "minimum depth" reads at thi
  4 KB (547 words) - 16:10, 23 February 2012
• RvTests
  PERMUTATION : --nPermute [10], --PermutationSeed [1] --All: specifies 1 to include all variants and 0 to include only nonsyn and stop annotated var
  4 KB (623 words) - 22:59, 13 January 2015
• Relationship between Ploidy, Alleles and Genotypes
  F(P,A) = \binom{P+A-1}{A-1} \\ G(a_1,.. , a_P) = \sum_{k=1}^P \binom{k+a_k-1}{a_k-1}
  11 KB (1,773 words) - 21:07, 18 October 2017
• Mach DAC
  ...mb is that minimac should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 100 haplotypes, see [http://ge
  2 KB (321 words) - 11:24, 2 February 2017
• M3VCF Files
  ...the variable <code>REPS</code>) which are the four sub-columns (of 0's and 1's) under the <code>FORMAT</code> column. Similarly, the 2 unique haplotypes ##version=1.1
  6 KB (799 words) - 20:35, 29 January 2015
• Rare variant tests
  1. Aggregate tests (typically with 1% threshold, nonsynonymous SNPs probably 1% threshold, nonsynonymous SNPs only, with meta-analysis
  7 KB (933 words) - 11:35, 2 February 2017
• Vmatch
  vmatch <vcf-file-1> <vcf-file-2> -g <genome-file> -w <int> -d vcf-file-1 VCF file (can be gzipped or bgzipped)
  5 KB (649 words) - 17:11, 23 January 2012
• 830 - Haplotyper::ScoreLeftConditional()
  for (int i = 1; i < markers; i++) Transpose(leftMatrices[i-1], leftMatrices[i], thetas[i-1]);
  453 bytes (39 words) - 13:30, 2 October 2013
• Ligate Minimac
  1) You are attempting to merge only minimac chunks from the same chromosome i.e. chr9.1.10000.info.gz and chr9.1.10000.dose.gz
  1 KB (246 words) - 15:06, 10 September 2013
• C++ Class: CigarRoller
  The queryIndex is the index in the read - from 0 to (read length - 1). refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
  5 KB (712 words) - 12:00, 2 February 2017
• VcfRefGen
  Source code can in: [[Media:vcfRefGen.0.1.4.tgz‎|VcfRefGen.0.1.4.tgz‎]] - Released 09/04/2014 * [[Media:vcfRefGen.0.1.3.tgz‎|VcfRefGen.0.1.3.tgz‎]] - Released 01/29/2013
  2 KB (332 words) - 15:53, 4 September 2014
• RAREMETAL METHOD
  <math>U_{meta_i}=\sum_{k=1}^S {U_{i,k}}</math> <math>V_{meta_i}=\sum_{k=1}^S{V_{ii,k}}</math>.
  6 KB (1,048 words) - 13:28, 20 May 2019
• BamUtil: readIndexedBam
  ...] executable reads an indexed BAM file reference id by reference id, from -1 to the max reference id and writes it out as a SAM/BAM file. {{BamIndex|noParam=3rd|required=1}}
  1 KB (170 words) - 17:48, 6 January 2014
• RelativeFinder
  MZTWIN 1 0 0 1 0 MZTWIN TEST1 1 2 1 MZ
  6 KB (796 words) - 04:17, 23 November 2010
• LiftRsNumber.py
  sys.exit(1) h, l = fd[0], fd[1]
  2 KB (287 words) - 11:33, 10 August 2011
• Haploxt
  Sample haplotype file 1:<br> ...values are calculated for each SNP. Default is 1,000, meaning that LD with 1,000 SNPs on each side (2,000 total) will be calculated for each SNP. <br>
  4 KB (510 words) - 18:22, 21 October 2010
• BamUtil: filter
  For mismatch threshold, the logic goes in 1 match/mismatch base at a time from each end of the read and checks its curr :<math>{1 \over 1 + 0} = {1 \over 1} = 1</math>
  10 KB (1,546 words) - 14:07, 6 January 2014
• BamUtil: polishBam
  ...010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none" @SQ SN:1 LN:2004
  7 KB (1,103 words) - 14:06, 6 January 2014
• RAREMETALWORKER METHOD
  <math> U_i=(\mathbf{G_i}-\mathbf{\bar{G_i}} )^T \hat{\boldsymbol{\Omega}}^{-1}(\mathbf{y}-\mathbf{X}\boldsymbol{\beta}) </math> ...bol{\Omega}}^{-1}\mathbf{X})^{-1} \mathbf{X^T} \hat{\boldsymbol{\Omega}}^{-1})(\mathbf{G}-\bar{\mathbf{G}}) </math>.
  6 KB (902 words) - 17:49, 16 March 2018
• 830 - Haplotyper::ScoreLeftConditional() (smart, complicated)
  for (int i = 1; i < markers; i++) theta = theta + thetas[i - 1] - theta * thetas[i - 1];
  966 bytes (97 words) - 14:31, 2 October 2013
• MappabilityScores
  ...as "non-unique" otherwise. Position X in the alignable track is marked by 1 if >50% of the bases in [X-200,X+200] are "unique" and by 0 otherwise. Ever ...first base of the sequence. Scores are normalized to between 0 and 1 with 1 representing a completely unique sequence and 0 representing the sequence o
  3 KB (499 words) - 07:17, 18 March 2010
• 830 - BestAlignment::MaqAlignment()
  position = -1; double quality = pow(10.0, -0.1 * sumQ) / (mapQdenominator + 1e-30);
  1 KB (126 words) - 13:45, 28 October 2013
• Bayesdenovo
  *** This build (v.0.1) was compiled on Oct 25 2016, 11:16:22 *** Input : --in_vcf [], --submap [1.00]
  6 KB (900 words) - 10:22, 26 October 2016
• SeqShop: Ancestry On Your Own Genome, May 2015
  === Step 1: bam --> pileup === This step takes ~1 hour for a genome sequenced at 17X.
  5 KB (733 words) - 14:57, 21 May 2015
• 830 - Haplotyper::ImputeGenotypes() (edge)
  posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; posterior[haplotypes[j][marker] + 1][marker] += *matrix;
  673 bytes (71 words) - 16:16, 2 October 2013
• BamPileup
  Filters : --min_mapq [0], --min_bq [0], --min_dp [0], --max_dp [-1],
  501 bytes (63 words) - 18:08, 28 February 2013
• Summary Statistics Files Specification for RAREMETAL and rvtests
  ...TAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file. ##SEX 1 1 2 2 2 1.5764 0.244204
  8 KB (658 words) - 11:39, 29 August 2019
• SplitPed
  Window size can be specified by one of the following three options: (1) -nWindows (2) -windowSize and (3) -windowLength. <br> ...region on each side can be specified by one of the following two options: (1) -overlapSize and (2) -overlapLength. <br>
  4 KB (538 words) - 11:33, 2 February 2017
• Understanding QPLOT output
  DupRate(%) 1.39 1.39 colvec=c(1,2);
  3 KB (299 words) - 10:03, 23 October 2014
• StatsTools
  {|border="1" cellspacing="0" cellpadding="2" The software returns 0 on completion, or -1 if the parameters could not be read or there was a problem reading an input
  4 KB (662 words) - 17:17, 1 June 2012
• BamUtil: writeRegion
  Specify -1 for unmapped Defaults to -1: meaning from the start of the reference.
  6 KB (833 words) - 12:30, 6 January 2014
• SeqShop: Ancestry On Your Own Genome, June 2014
  === Step 1: bam --> pileup === === Step 1: bam --> pileup ===
  3 KB (464 words) - 14:32, 13 November 2014
• CalcMatch
  generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of over (1) SNP&nbsp;: SNP name
  5 KB (686 words) - 12:03, 2 February 2017
• Minimac Diagnostics
  ...ele 1 - this corresponds to the average number of imputed copies of allele 1 for each individual, divided by two. :<math>\hat{r}^2 = {{Var(\mbox{Estimated Counts})}\over{\hat{p}(1-\hat{p})}}</math>
  2 KB (355 words) - 11:35, 8 June 2017
• C++ Class: SamFile
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ...ments that were successfully read from the file with FLAG bit 0x001 set to 1 (paired).
  4 KB (572 words) - 11:03, 2 February 2017
• 830 - Haplotyper::ImputeGenotypes() (internal)
  posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; posterior[haplotypes[j][marker] + 1][marker] += *matrix1 * *matrix2 * 0.5;
  860 bytes (86 words) - 16:15, 2 October 2013
• Thunder
  samtools pileup -g -T 1 -f ref.fa my.bam &gt; my.glf This variant calling pipeline has two steps. (step 1) promotion of a set of potential polymorphisms; and (step 2) genotype/haplo
  4 KB (605 words) - 12:08, 21 February 2017
• Tutorial: Low Pass Sequence Analysis Answers
  @ERR020230.76497044/1 33514465 T C GT:GD:GQ:PL 1/1:3:10:117,9,0
  6 KB (849 words) - 04:10, 23 June 2016
• Famrvtest
  1 1 0 0 1 1.5 1 23 A A A A A A A A A A 2 1 0 0 1 1.0 1 34 A C A C A C A C A C
  7 KB (1,065 words) - 10:34, 21 February 2017
• Verifying Sample Identities - Implementation
  {| width="100%" cellspacing="1" cellpadding="1" border="1" summary="Summary of Variables Used Below" ...sequenced sample and the target sample share a chromosome. This should be 1.0 when we have sequenced the correct sample and 0.0 if we sequence an unrel
  4 KB (741 words) - 10:25, 29 April 2010
• RAREMETALWORKER X
  ...ust be coded in the format of 1/1, 0/0, or be coded to be haploids as 0 or 1. Any heterozygous male genotypes are treated as missing and imputed to the
  2 KB (358 words) - 19:13, 27 March 2014
• Understanding VerifyBamID output
  SRR062634 5 1 0.00003 0.00003 SRR062634 4 1 0.00003 0.00006
  7 KB (538 words) - 16:48, 4 March 2013
• Test EPACTS for DIAGRAM
  <pre>cd epacts2.1/ <pre>$ epacts2.1/epacts help
  7 KB (841 words) - 10:28, 2 February 2017
• SeqShop: Ancestry On Your Own Genome, December 2014
  === Step 1: bam --> pileup === This step takes ~1 hour for a genome sequenced at 17X.
  5 KB (821 words) - 12:43, 12 December 2014
• Ancestry
  1 752566 rs3094315 G A 1 768448 rs12562034 G A
  4 KB (566 words) - 14:53, 12 August 2014
• GWAS
  ...xamined evidence for association between a trait of interest and 100,000 - 1,000,000 genetic variants distributed across the genome. They have been quit
  410 bytes (55 words) - 11:39, 30 March 2010
• Tutorial: EMMAX GotCloud STOM: Lecture 2
  > qchisq(0.4814,1,lower.tail=FALSE) [1] 0,4956901
  4 KB (623 words) - 03:07, 6 January 2014
• 830 - MarkovModel::Condition()
  double pmatch = (1. - e) + e * freq;
  440 bytes (50 words) - 14:40, 25 September 2013
• Minimac3 Info File
  '''For versions earlier than 0.1.13 (downloaded before Oct 15, 2015 or from Imputation Server) please see [[ ==='''REF(0)''', '''ALT(1)'''===
  8 KB (1,162 words) - 17:48, 14 December 2018
• GotCloud: AMIs
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | 1.14.4|| ami-6ae65e02 || gotcloud.1.14.4.public || 196677801509 || h37-db135-v3.tgz || starcluster-base-ubuntu-
  403 bytes (49 words) - 15:56, 30 October 2014
• SplitRef
  Window size can be specified by one of the following three options: (1) -nWindows (2) -windowSize and (3) -windowLength. <br> ...region on each side can be specified by one of the following two options: (1) -overlapSize and (2) -overlapLength. <br>
  3 KB (398 words) - 11:34, 2 February 2017
• GTDT
  --max_avg_dp [0.00], --max_missing_rate [1.00], Multi-threading : --nthreads [1]
  7 KB (821 words) - 08:18, 26 March 2015
• LibStatGen: general
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
  2 KB (223 words) - 10:51, 2 February 2017
• Sam Library Usage Examples
  exit(-1); samIn.OpenForRead(argv[1]);
  11 KB (1,206 words) - 09:07, 7 September 2011
• LibStatGen: VCF
  // Subset 1 is delimited by new lines, '\n'. // Subset 1 is delimited by new lines, '\n'.
  18 KB (2,634 words) - 16:09, 23 January 2013
• GotCloud: Genetic Reference and Resource Files
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
  8 KB (1,291 words) - 12:00, 14 May 2015
• Git Cheat Sheet
  {| border="1" align="left" style="border-collapse: collapse;" | 1) Stage Changes
  3 KB (414 words) - 19:13, 7 July 2011
• DosageConvertor
  * '''Download/Re-Clone Release Version 1.0.4 (Updated July 2017) !''' '''VERSION: 1.0.4 (Updated 7.12.2017) !'''
  8 KB (1,151 words) - 14:01, 18 January 2019
• BamUtil: splitChromosome
  Reference Name: 1 has 5 records Reference Name: 3 has 1 records
  2 KB (289 words) - 17:43, 3 January 2014
• LiftMap.py
  fo.write('%s\t%d\t%d\t%s\n' % (chrom, pos-1, pos, rs)) UNLIFTED_SET.add(ln.strip().split()[-1])
  4 KB (613 words) - 23:18, 18 June 2012
• Pileup
  1. CHROM : chromosome. d. BASEQ : phred quality score, -1 for deletions.
  3 KB (434 words) - 15:06, 3 April 2012
• BamUtil: trimBam
  Version 1.0.6 and later: Available in version 1.0.14 and later.
  7 KB (1,105 words) - 23:28, 12 November 2017
• Code Sample: Generating QQ Plots in R
  ...get from tests where no true association exists should follow a uniform(0,1) distribution. Since we're usually most interested in really small p-values distribution=function(x){-log10(qunif(1-x))}
  9 KB (1,398 words) - 14:14, 12 November 2013
• LibStatGen: ASP
  Every record starts with a 1-byte field. The lower 4 bits indicate the type and for some types, the upp ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
  19 KB (2,589 words) - 11:45, 30 April 2012
• PileupBasedVariantCalling
  ...enomic position, it will produce pileups containing the information about (1) base reads and strands (2) base qualities (3) mapping qualities and (4) cy 1 10002
  7 KB (1,018 words) - 15:52, 10 September 2013
• BamUtil: bam2FastQ
  Read Names in paired-end FASTQ files are appended with "/1" for the first in the pair, and "/2" for the second in the pair. Override ...c FASTQ files, first run [[BamUtil: splitBam]] to first split the BAM into 1 BAM per Read Group. Then run bam2FastQ on each bam.'''
  13 KB (1,798 words) - 23:53, 5 March 2016
• RareMETALS
  ...sed. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consid * 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where th
  18 KB (2,053 words) - 10:18, 18 May 2017
• LASER
  This page was created for LASER 1.0. Some of the information might be outdated for LASER 2.0. LASER typically outputs two coord files: (1) in reference individuals' coord file(Reference.coord), LASER outputs the r
  12 KB (1,605 words) - 11:51, 2 February 2017
• SAM: Filtering Reads
  refOffset: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 queryIndex: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15...
  4 KB (434 words) - 17:25, 21 September 2010
• Variant Call Pipeline
  {| border="1" | STEPS || 1,2,3,4,5,6,7,8 || Describe which steps will be executed
  7 KB (907 words) - 15:36, 21 December 2010
• Minimac3
  '''VERSION: 2.0.1 !!! (Updated 6.6.2016) !!!''' {| class="wikitable" style="text-align:center" border="1" cellpadding="2"
  7 KB (1,080 words) - 15:40, 18 October 2022
• GlfSingle
  **P(non-reference homozygote) = 0.01 * 1/3 **each transversion has 1/6 probability
  3 KB (404 words) - 11:34, 26 September 2013
• Genotype Likelihood based Hardy-Weinberg Test
  ...> and <math>j</math> . <math>k</math> indexes the individuals from <math>1</math> to <math> N</math> . -2logL(R|g) \sim X^2_v, v = \frac{n(n-1)}{2}
  2 KB (320 words) - 15:52, 3 August 2015
• Minimac4 Documentation
  Other Parameters : --log, --help, --cpus [1], --params :* '''DS''' - Estimated alternate allele dosage [P(0/1)+2*P(1/1)].
  8 KB (1,095 words) - 23:17, 19 July 2019
• BamUtil: FAQ
  make[2]: *** [../obj/HashErrorModel.o] Error 1 # Update bamUtil/Makefile.inc, line 7, change <code>CXX11_AVAIL ?= 1</code> to <code>CXX11_AVAIL = 0</code>
  4 KB (605 words) - 13:04, 23 September 2014
• Using Gotcloud on Flux
  1. Install GotCloud somewhere as instructed [[GotCloud#GotCloud_Setup_on_Any_ ...pvcfN, filtN, svmN, splitN, allN where N is the name of a chromosome (ie, 1-22 and maybe X and Y). If you skip a step, it's not a problem, because <co
  6 KB (941 words) - 11:51, 12 January 2016
• MutationFilter
  Cycle Bias (CB) : --mut_median_cycles2ends [-1] Strand Bias (SB) : --SB_OR [-1.0e+00]
  8 KB (1,107 words) - 01:06, 16 April 2013
• ChunkChromosome
  awk '{ if ($1 == "M") print $2; }' < chr1.dat > chr1.snps foreach chr (`seq 1 22`)
  3 KB (435 words) - 10:02, 2 February 2017
• M3vcftools Usage
  {| border="1" cellpadding="2" {| border="1" cellpadding="2"
  6 KB (938 words) - 22:04, 18 October 2015
• BamUtil: diff
  1) the specified name with record diffs Set to -1 for unlimited number of records
  11 KB (1,845 words) - 17:00, 6 January 2014
• Editing Sequence Analysis Practice 2011/03/10
  1. EXON-TARGETTED DATA : COMPUTING GENOTYPE LIKELHOOD FROM BAM FILES ...78.exon.sample.vcf ${OUT}/NA12878.highcov.sample.vcf | grep -v ^# | cut -f 1,2 | sort | uniq -d | wc -l
  3 KB (388 words) - 02:14, 10 March 2011
• BAM to FASTQ
  One file for the first in pair & 1 file for the 2nd in the pair - the order in the two files must match. ** Prefer to sort at the same time as writing the FASTQ files rather than 1 step to sort and a 2nd step to write the FASTQs.
  3 KB (455 words) - 10:45, 10 June 2013
• Tandem Repeat Concepts
  shift 1: CACAA motif_concordance : 1
  8 KB (798 words) - 19:17, 25 February 2016
• Variant classification
  ;1. SNP : The reference and alternate sequences are of length 1 and the base nucleotide is different from one another.
  15 KB (1,324 words) - 21:44, 25 February 2016
• Power Calculations: Quantitative Traits
  ..._i </math> denoting the observed genotype for each individual (coded as 0, 1 or 2 according to the number of copies of the rare alelele). threshold = qchisq(alpha, df = 1, lower.tail = FALSE)
  3 KB (423 words) - 11:02, 17 June 2010
• FTEC
  1) Download the appropriate file below <br> 1) Instructions for Installing MinGW and MSYS can be found here: [[Installing
  3 KB (407 words) - 11:21, 17 February 2012
• Phred scale
  ...phredScore = 20. A base call expected to be accurate 99.9% of the time (0.1% error rate), would be assigned a phredScore = 30.
  449 bytes (70 words) - 16:17, 23 March 2010
• SardiNIA project meeting July 15-16, 2013
  ....metrocars.com/michigan/reservations/index.asp Metro Cars] 734-946-5700 or 1-800-456-1701 [http://www.metroairporttaxi.org/reservations.htm Metro Airport Taxi] 1-800-745-5191
  4 KB (694 words) - 11:46, 8 July 2013
• GLF
  GLF files can be generated using [https://github.com/statgen/samtools-0.1.7a-hybrid samtools-hybrid]. To generate a GLF file, use the <code>samtools- ...// Printable string identified the chromosome label; typically, "1", "2", "3"... "22", "X", "Y", "MT" are used as labels for human chromosomes
  8 KB (1,103 words) - 11:22, 13 August 2013
• 830 - BasicMapper::main()
  String mask1('1', indexComplexity), mask0('0', indexComplexity), mask; if (best.mismatches == 1) mapMismatchesEq1++;
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• Bam read count
  Mapping filters : --min_overlap [1], --min_map_quality 1 1000 2000 GENE1
  4 KB (536 words) - 15:29, 14 August 2012
• RareMETALS2
  * 1.) It allows the meta-analysis of samples with related individuals and sampl June, 14, 2015 0.1 Version released
  13 KB (1,350 words) - 15:11, 29 June 2015
• CheckVCF.py
  version 1.3 (20130223) [ 1 ] Alternative allele frequency &gt; 0.5 sites are outputted to [ tmp.check.
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• Tutorial: RAREMETAL
  ==STEP 1: Install Software and Download Example Data Sets== tabix -c "#" -s 1 -b 2 -e 2 STUDY1.QT1.singlevar.score.txt.gz
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• VcfCodingSnps
  1. Get into folder "libcsg". Type syntax "gcc -c -O2 *.cpp -D_FILE_OFFSET_BIT 1. Example headlines of input VCF-format SNP file:
  14 KB (1,768 words) - 11:58, 2 February 2017
• An example of using libcsg
  The purpose of this program is (1) to extract a range of text from a input file, and count there frequencies. for (int i = 1; i < haplos.Length(); i++)
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• BamUtil: validate
  ...just want to know if the file is validly formatted or not, use --maxErrors 1 -1 (default) indicates to not quit until the entire file is validated.
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• Genotype Likelihood Based Allele Balance
  nref_i = 0.5 * depth_i * (1 + {(lss_i - lrr_i)\over lss_i + lrr_i - 2 * lrs_i + 6 * depth_i}) \
  626 bytes (89 words) - 15:22, 22 October 2010
• SAM Validation Criteria
  {| class="wikitable" style="width:100%" border="1" | SQ/LN is in the range [1, (2^29) -1]
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• TinySimulator
  ; --mutationRate 1.0e-8 ; --recombRate 1.0e-8
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• 830 - MINIMAC::main()
  int stopIndex = reference.markerCount - 1; for (int i = 0; i < reference.markerCount - 1; i++)
  12 KB (1,088 words) - 15:06, 2 October 2013
• How to use aspera
  1. use ascp under your directory: ~/.aspera/connect/bin/ascp
  953 bytes (146 words) - 00:56, 9 May 2013
• Indel
  ...nt, although not quite as abundant as SNPs. It is estimated that there are 1-2 million short indels segregating at low to high frequency in modern human
  650 bytes (87 words) - 20:44, 30 May 2010
• Triodenovo
  Denovo mutation rate : --mu [1.0e-07] Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]
  8 KB (1,165 words) - 18:19, 11 January 2023
• Example
  1. Prepare the input files using prepare012s
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• Using Git Example
  {| style="width: 1200px" border="1" {| style="width: 1200px" border="1"
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• Minimac4
  ...nly applicable to version 4.0.x (a.k.a 1.0.x). Documentation for version 4.1.x can be found on the [https://github.com/Santy-8128/Minimac4 Minimac4 Gith '''Minimac4 (version 1.0.0, released 2.14.2018)''' is currently available on [https://github.com/S
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• SAM
  ...the reference, POS. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. B ...ence, MPOS or PNEXT. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. B
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• TabAnno
  ...--tabix : Specify the tabix file and tag (e.g. abc.txt.gz(chrom=1 1 10 20 a
  14 KB (1,969 words) - 11:57, 2 February 2017
• GotCloud: Configuration
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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• Analyses of Indels
  ...cf-binary-vcf-version-2 BCFv2.1]] of the Variant Call Format (VCF). BCFv2.1 is more efficient to process as the data is already stored in computer read The VCF file you work with should preferably be BCF2.1 compatible. Here we provide an example in /net/fantasia/home/atks/indel_an
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• EMMAX
  *# Beta (1 is effect allele) ...ept has to be included, meaning that the third column is recommended to be 1 always, and the covariates needs to be included from the fourth column. The
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• FamLDCaller
  1. Update the algorithm to allow nuclear and multi-generational pedigrees ...he state space. The default is the maximum number: 2*(number of founders -1).
  3 KB (435 words) - 10:05, 18 August 2014
• RAREMETAL FAQ
  collect2: ld returned 1 exit status make: *** [../bin/raremetal] Error 1
  7 KB (1,054 words) - 11:46, 20 March 2018
• UMAKE-glfSingle
  .../glfSingle -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference > $smVcf.log"); ...ngle_ut''' -g $smGlf -b $smVcf -l $allSMs[$i] --minMapQuality 0 --minDepth 1 --maxDepth 100000 --reference '''--uniformTsTv''' > $smVcf.log");
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• LibStatGen: GLF
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
  1 KB (214 words) - 11:01, 2 February 2017
• Fst
  :<math>F_{st} = (p_1 - p_2)^2 / {2\overline{p}(1-\overline{p})}</math>
  799 bytes (113 words) - 03:47, 3 October 2010
• BamUtil: stats
  Defaults to -1 to indicate all reads. ...imum number of reads to process before exiting. By default, it is set to -1 to indicate all reads should be processed.
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• SeqShop: Estimates of Genetic Ancestry Practical, May 2015
  === Step 1: bam --> pileup === # $LASER/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
  8 KB (1,248 words) - 09:57, 2 February 2017
• MaCH FAQ
  ...illion markers for 1000 individuals using 100 reference haplotypes takes ~ 1 hour; and computing time increases linearly with all the above three parame ...you can use MaCH-Admix, which does not require pre-phased data and takes ~1/7 of the computing time of that typically needed for pre-phasing. For large
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• Code Sample: Generating Manhattan Plots in R
  posshift <- head(c(0,cumsum(posmax)),-1); if(nchar(rawval)>=1) {
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• Screen Commands
  {| border="1" cellspacing="0" cellpadding="2"
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• 1000 Genomes Project Pilot 1 SNP Calling
  == (1) Create GLF files from BAM files == /home5/2009.08.GLF-1/
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• Sequence Analysis Practice 2011/03/09
  1. Understanding FASTQ format 1. EXON-TARGETTED DATA : COMPUTING GENOTYPE LIKELHOOD FROM BAM FILES
  6 KB (840 words) - 13:29, 10 March 2011
• GotCloud: FAQs
  ...tory `/group/onel-lab/GeneticResources/bin/gotcloud/1.16/gotcloud-gotcloud.1.16/src/samtools'<br />make<nowiki>:</nowiki> *** [samtools] Error 2 :*#: <code>-D_CURSES_LIB=1</code>
  12 KB (1,871 words) - 10:54, 23 June 2015
• C++ Class Averages
  median = -1; if(median == -1)
  2 KB (169 words) - 12:27, 2 August 2010
• BAFRegress
  ...h the allele frequency for one of the two alleles with a value between 0.0-1.0 or NA if missing. * --colab1=col, AB Allele 1 column [default: Allele1 - AB]
  7 KB (1,182 words) - 17:09, 18 July 2018
• Sequencing Workshop Analysis of Indels
  ...cf-binary-vcf-version-2 BCFv2.1]] of the Variant Call Format (VCF). BCFv2.1 is more efficient to process as the data is already stored in computer read ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
  14 KB (1,740 words) - 16:47, 16 June 2014
• GotCloud: Variant Calling Pipeline
  # BAM File 1 (preferable to have full paths to BAM files) # BAM File 2 (if more than 1 BAM per sample)
  8 KB (1,270 words) - 18:54, 30 March 2015
• BamUtil: dumpHeader
  @SQ SN:1 LN:247249719
  1 KB (150 words) - 16:50, 6 January 2014
• SeqShop: Estimates of Genetic Ancestry Practical, June 2014
  === Step 1: bam --> pileup === # ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
  10 KB (1,458 words) - 10:23, 2 February 2017
• BamUtil: recab
  * Additional criteria for cycle != 1 (can be turned off via flags) * at least 1 match or mismatch for the set of covariates
  13 KB (1,670 words) - 23:01, 19 April 2019
• GotCloud: Alignment Sub-Pipelines
  # BAM File 1 (preferable to have full paths to BAM files) # BAM File 2 (if more than 1 BAM per sample)
  20 KB (3,030 words) - 21:37, 18 March 2015
• SeqShop: Estimates of Genetic Ancestry Practical, December 2014
  === Step 1: bam --> pileup === # $LASER/laser -g $HGDP/HGDP_938.geno -pca 1 -k 30 -o HGDP_938
  10 KB (1,511 words) - 10:24, 2 February 2017
• Variant Normalization
  ...variant is non parsimonious, all its alleles must have length greater than 1. ...to detect if a variant is normalized, we first prove the following lemma (1).
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• Parameters.h
  int anInteger = 0, anotherInteger = 1;
  1 KB (142 words) - 03:26, 26 November 2009
• MEAGA
  {| border="1" cellpadding="5" cellspacing="0" align="center" A 1-column file for the best signals identified in the genetic association stud
  9 KB (1,307 words) - 21:37, 4 March 2015
• Biostatistics 615/815 Fall 2011
  * Lecture 1 : Introduction to Statistical Computing -- [[Media:Biostat615-Fall2011-lect ...a:Biostat615-lecture11-2011-10-20.pdf | (PDF)]] '''(UPDATED on Oct 28th at 1:42PM)'''
  11 KB (1,312 words) - 17:35, 31 August 2012
• GotCloud: GenomeSTRiP Pipeline
  # BAM File 1 (preferable to have full paths to BAM files) # BAM File 2 (if more than 1 BAM per sample)
  14 KB (1,857 words) - 18:47, 10 February 2015
• LiftOver
  (1) [[#Lift genome positions | Convert genome position from one genome assembl awk '{print $1,$2,"\t",$3;}' PLINK.map > Merlin.map
  14 KB (2,263 words) - 18:33, 15 July 2015
• EPACTS for DIAGRAM
  ...stical tests we will use for for analysis of low frequency variants:&nbsp;(1) logistic regresion-based score test and (2) Firth bias-corrected logistic == 1. &nbsp;Download and install EPACTS ==
  24 KB (3,442 words) - 10:05, 2 February 2017
• FastQValidator
  [[Media:fastQValidatorLibStatGen.0.1.1a.tgz|fastQValidatorLibStatGen.0.1.1a.tgz‎]] - Released 11/13/2012 '''fastQValidatorLibStatGen.0.1.1a Release Notes'''
  11 KB (1,458 words) - 11:00, 2 February 2017
• Minimac Command Reference
  ...erence); upper and lower case letters are treated identically. The digits "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G ...first of these columns denotes the probability of an homozygote for allele 1. The second column denotes the probability of an heterozygote.
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• Polymutt2
  --max_avg_dp [-1.0e+00], --max_missing_rate [0.05] Mutation paramters : --theta_snv [1.0e-03], --theta_indel [1.0e-04],
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• Polymutt
  ..., for each genotype, a genotype quality (GQ) value is defined as -10*log10(1-posterior(Genotype | Data)). ...y helpful to explore various mutation rate in addition to the default one (1.5x10-8). For depth lower than 30X for example, the support of ''de novo'' m
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• RAREMETAL Documentation
  tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.score.txt.gz tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz
  24 KB (3,256 words) - 13:22, 20 May 2019
• Biostatistics 602: Main Page
  ...tations and higher order moments, random sampling. (approximately chapters 1-5.5 of Casella and Berger.) Classes are scheduled for Tuesday and Thursdays, 1:00 - 3:00pm at USB 2260
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• GotCloud: Variant Calling Options
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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• Vpeep
  ##fileformat=VCFv4.1 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples with Fully Called Data">
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• RAREMETALWORKER
  --maleLabel [1], --femaleLabel [2] others : --cpu [1], --kinOnly,
  18 KB (2,478 words) - 13:34, 20 November 2019
• EMADS Primary Analysis Plan
  {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" === (1) Average cigarettes smoked per day, either as a current smoker or former sm
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• SeqShop: June 2014
  | [[Media:Analysis of SV.pdf|Analysis of Structural Variation - Part 1]]
  2 KB (264 words) - 14:21, 13 November 2014
• QPLOT
  (1) Download the pre-compiled binary along with the source code as described i ...nxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]
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• Regions of high linkage disequilibrium (LD)
  ...ods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These r <tab border="1" head="top">
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• Genezoom
  1. cd pathToYourCopy/geneZoom Version : 1.0.1
  7 KB (1,057 words) - 11:40, 16 March 2016
• SeqShop: Genetic Association Analysis Practical, June 2014
  HG00640 HG00640 0 0 0 1 HG00641 HG00641 0 0 0 1
  19 KB (2,551 words) - 10:27, 2 February 2017
• C++ Class: SamFileHeader
  A SAM Header can have 0 or 1 HD records, 0 or more PG records, 0 or more SQ Records, and 0 or more RG re
  2 KB (322 words) - 11:05, 2 February 2017
• Minimac3 Imputation Cookbook
  ...nce panels are 1000 Genomes Phase 3 (2,535 samples), 1000 Genomes Phase 1 (1,094 samples), HapMap2 (269 samples), Haplotype Reference Consortium (32,914
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• SardiNIA
  We are sequencing the genomes of 1,000 individuals to learn about the genetics of blood lipid levels and perso * '''PheWAS: GWAS on 120 traits for Visit 1'''
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• BamUtil: squeeze
  ...are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70 ...are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70
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• SeqShop: Association Analysis, May 2015
  HG00640 HG00640 0 0 0 1 HG00641 HG00641 0 0 0 1
  20 KB (2,538 words) - 14:15, 21 May 2015
• BamUtil: findCigars
  Number of records written = 1
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• MaCH: 1000 Genomes Imputation Cookbook
  foreach chr (`seq 1 22`) foreach chr (`seq 1 22`)
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• RAREMETALWORKER command reference
  --maleLabel [1], --femaleLabel [2] others : --cpu [1], --kinOnly,
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• IMPUTE2: 1000 Genomes Imputation Cookbook
  CHR=$1 sge ./prototype_phasing_job.sh 1 1 5000000
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• SeqShop: Genetic Association Analysis Practical, December 2014
  HG00640 HG00640 0 0 0 1 HG00641 HG00641 0 0 0 1
  21 KB (2,694 words) - 10:27, 2 February 2017
• Evaluating a Read Mapper on Simulated Data
  *Reads with 1, 2, 3 or more SNPs.
  1 KB (223 words) - 23:19, 8 September 2010
• Meta Analysis of SNPxEnvironment Interaction
  ...nd SNP x environment regression coefficients. Genet Epidemiol. 2011 Jan;35(1):11-8. ...st/ http://toby.freeshell.org/software/quicktest/]) and ProbABEL version 0.1-3 and later ([http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/ http://mga.bion
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• LibStatGen: FASTQ
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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• Minimac: 1000 Genomes Imputation Cookbook
  ...format by default GWAS SNPs are expected to be in the chr:pos format e.g. 1:1000; otherwise, for GWAS SNPs in the rs format you have to set the --rs fl {| class="wikitable" border="1" cellpadding="2"
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• BamUtil: clipOverlap
  {|border="1" cellspacing="0" cellpadding="2" {|border="1" cellspacing="0" cellpadding="2"
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• Examples of Read Mapping with Karma and BWA
  {| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" | # (1) read mapping using karma
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• ContaminationDetection
  * Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modi
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• BAM Review Action Items
  if(!samIn.OpenForRead(argv[1])) samIn.OpenForRead(argv[1]);
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• VICES
  ...lele1-col <string> Name of report file column containing allele 1
  6 KB (787 words) - 09:59, 15 April 2019
• GotCloud: Alignment Pipeline
  ...ere is one line per single-end read and one line per paired-end read (only 1 line per pair). * FASTQ1 - name of the fastq or the first in the pair if paired-end. (Only 1 line per pair)
  13 KB (2,051 words) - 18:39, 28 January 2016
• SeqShop: May 2015
  | [[Media:Analysis of SV May2015.pdf|Analysis of Structural Variation - Part 1]]
  3 KB (411 words) - 10:40, 22 May 2015
• SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015
  ...the APOL1 gene. It has smaller than '''g1''' but still large effect size (>1.5 fold). Let's see if we have found the variant. ${GC}/bin/tabix ${OUT}/indel/final/all.genotypes.vcf.gz 22:36662041 | head -1
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• Basic Linux Intro
  {| border="1"
  3 KB (437 words) - 15:46, 26 July 2011
• SeqShop: December 2014
  | [[Media:Dec2014 Analysis of SV.pdf|Analysis of Structural Variation - Part 1]]
  3 KB (418 words) - 12:17, 18 December 2014
• Minimac2
  ...b is that minimac2 should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 1000 haplotypes (>10x faster t {| class="wikitable" border="1" cellpadding="2"
  13 KB (2,050 words) - 12:53, 9 March 2018
• GotCloud: Binary Releases
  Setting up gotcloud-bin (1.0) ... rsync -av --delete $tempdir/usr/local/gotcloud/* $destdir/gotcloud || exit 1
  15 KB (2,137 words) - 23:29, 7 January 2016
• Rvtests
  ...r />For binary trait, the recommended way of coding is to code controls as 1, cases as 2, missing phenotypes as -9 or 0. * Burden tests: group variants, which are usually less than 1% or 5% rare variants, for association tests. The category includes: CMC tes
  29 KB (4,420 words) - 00:31, 12 May 2016
• SeqShop: Variant Calling and Filtering for INDELs Practical, December 2014
  ...the APOL1 gene. It has smaller than '''g1''' but still large effect size (>1.5 fold). Let's see if we have found the variant. ${GC}/bin/tabix ${OUT}/indel/final/all.genotypes.vcf.gz 22:36662041 | head -1
  24 KB (3,267 words) - 17:09, 17 December 2014
• LibStatGen Download
  '''LibStatGen.1.0.14 Release Notes''' *Version 1.0.14 - Released 7/8/2015
  10 KB (1,430 words) - 00:04, 13 November 2017
• RAREMETAL Command Reference
  QC Options : --hwe [1.0e-05], --callRate [0.95] --longOutput, --tabulateHits, --hitsCutoff [1.0e-06]
  3 KB (300 words) - 17:53, 16 March 2018
• Biostatistics 615/815 Winter 2011
  * Lecture 1 : Statistical Computing -- [[Media:Biostat615-lecture1-handout.pdf | (Hando ...e on January 20th, 2011 -- [[Media:Biostat615-homework1.pdf | (Problem Set 1 - PDF)]]
  36 KB (4,875 words) - 00:10, 6 September 2011
• Creating an AMI on EC2
  ..., at least for now it seems any StarCluster activity must be in '''us-east-1'''. ...de>-j #</code> based on the number of CPUs your instance has, if more than 1
  11 KB (1,759 words) - 14:54, 14 October 2014
• SeqShop: Analysis of Structural Variation Practical, June 2014
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). 1 COHERENCE;COVERAGE;PAIRSPERSAMPLE
  17 KB (2,452 words) - 14:37, 13 November 2014
• Biostatistics 615/815: Main Page
  * Lecture 1 : Introduction to Statistical Computing -- [[Media:bios615-fa12-lec01-hando * Problem Set 1 (Due September 22) : [[Media:bios615-fa12-hw1.pdf | (PDF)]] (revised on 9/1
  8 KB (1,077 words) - 21:53, 18 December 2012
• Karma
  {| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" | ...ments are not currently supported. These features will return in Karma 0.9.1.
  14 KB (2,190 words) - 11:10, 2 February 2017
• SeqShop: Variant Calling and Filtering for INDELs Practical, June 2014
  ...the APOL1 gene. It has smaller than '''g1''' but still large effect size (>1.5 fold). Let's see if we have found the variant. ${GC}/bin/tabix ${OUT}/final/all.genotypes.vcf.gz 22:36662041 | head -1
  22 KB (3,052 words) - 14:36, 13 November 2014
• SeqShop: Analysis of Structural Variation Practical, May 2015
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). -numjobs INT Number of jobs to concurrently run [1]
  20 KB (2,783 words) - 15:56, 25 August 2015
• SeqShop: Calling Your Own Genome, May 2015
  The list of BAMs has already been created (just 1 BAM, your sample). The list of BAMs has already been created (just 1 BAM, your sample).
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• LibStatGen: BAM
  ...olor: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
  4 KB (566 words) - 10:55, 2 February 2017
• RAREMETALWORKER SPECIAL TOPICS
  ...re RAREMETALWORKER analyze chromosome X correctly, '''male must be code as 1 and female must be coded as 2''' in [[RAREMETALWORKER#PED_and_DAT_Files | '
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• SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). <li><code>0|1</code>: Heterozygous</li>
  20 KB (2,959 words) - 14:37, 13 November 2014
• Minimac: Tutorial
  {| class="wikitable" border="1" cellpadding="2" {| class="wikitable" border="1" cellpadding="2"
  7 KB (1,087 words) - 12:34, 25 January 2017
• SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). * Beagle will take about 1-3 minutes to complete
  19 KB (2,813 words) - 18:35, 19 August 2015
• SeqShop: Analysis of Structural Variation Practical, December 2014
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). -numjobs INT Number of jobs to concurrently run [1]
  21 KB (2,922 words) - 17:09, 17 December 2014
• Tutorial: EMMAX GotCloud STOM: Lecture 8
  ...f $S5/examples/chr7Ref/hs37d5.chr7.fa --region 7:117000000-117500000 --run 1
  2 KB (400 words) - 02:31, 7 January 2014
• GotCloud: Creating a New Pipeline
  ...I_ONLY</code> - set to non-blank if step should run if there are more than 1 input per output. ...>SINGLE_ONLY</code> - set to non-blank if step should run if there is only 1 input per output.
  10 KB (1,525 words) - 14:55, 31 August 2015
• C++ Class: FastQFile
  ...ce and quality strings that wrap over multiple lines. It would only allow 1 line per raw sequence/quality string.
  4 KB (529 words) - 10:58, 2 February 2017
• Biostatistics 830: Fall 2013 Edition
  {| border="1" cellpadding="5" cellspacing="0" style="text-align: center;" ! style="background: lightgreen;" |1
  8 KB (1,143 words) - 13:59, 2 September 2014
• C++ Library: FASTQ Change Log
  {| style="width:100%; background:#FF8989; margin-top:1.2em; border:1px solid #ccc;" | * Update color space validation to require a 1 character primer base.
  3 KB (380 words) - 12:56, 1 May 2012
• SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014
  ...chr22 so the configuration already has <code>CHRS = 22</code> (default was 1-22 & X). * Beagle will take about 1-3 minutes to complete
  19 KB (2,942 words) - 19:12, 30 March 2015
• Minimac
  {| class="wikitable" border="1" cellpadding="2" ...mb is that minimac should take about 1 hour to impute 1,000,000 markers in 1,000 individuals using a reference panel with 100 haplotypes. Performance sh
  16 KB (2,442 words) - 12:53, 9 March 2018
• SeqShop: Aligning Your Own Genome, June 2014
  ls -1 ~/personal/Run_*/*/*R1* * The -1 option tells <code>ls</code> to list the matching files in a single column
  11 KB (1,960 words) - 14:25, 13 November 2014
• Exome Chip Design
  {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" | {| class="sortable wikitable" border="1" cellspacing="0"
  21 KB (2,877 words) - 07:42, 6 August 2013
• LocusZoom
  ; 1. Plot Summaries of Your Genomewide Scan Interactively ...ific distance (e.g. 500kb) of an index SNP. To use this option, set column 1 to have the name of the index SNP (e.g. ''rs2'' below) and set column 5 to
  15 KB (2,347 words) - 13:29, 28 October 2020
• Tutorial: GotCloud
  '''This tutorial is in the process of being updated for gotcloud version 1.08 (July 30, 2013).''' == STEP 1 : Setup GotCloud ==
  25 KB (3,744 words) - 12:35, 10 January 2014
• M3vcftools
  * '''Download Pilot Version 1.0.1 !!! (Updated Oct 2015) !!!''' See [[M3vcftools ChangeLog | ChangeLog ]] for '''VERSION: 1.0.1 !!! (Updated 10.25.2015) !!!'''
  3 KB (549 words) - 21:57, 10 July 2016
• RAREFY COMMAND
  Parameters : --maf [1.0e-03], --effect [1.00] default is '''1 SD'''; this option let you change the value of the fixed prior effect size
  3 KB (482 words) - 05:09, 17 February 2015
• BamUtil: dedup
  {{inBAMInputFile|noStdin=1}} Returns -1 if input parameters are invalid.
  9 KB (1,324 words) - 22:31, 8 April 2019
• UMAKE
  {| style="width:100%; background:#ffb6c1; margin-top:1.2em; border:1px solid #ccc;" | tar xzvf umake.v1.0.1.20110706.tar.gz
  16 KB (2,060 words) - 11:53, 2 February 2017
• EMADS
  {| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" ...had substantial individual contributions but not as much as those in Group 1. Typically, these might be lead analysts or other junior investigators who
  8 KB (1,152 words) - 23:03, 14 November 2013
• BamUtil
  For version 1.0.14 and later, please download libStatGen and bamUtil separately: '''Version 1.0.14 - Released 7/8/2015'''
  17 KB (2,168 words) - 17:14, 11 September 2021
• TrioCaller
  .... The examples are tested in in bwa 0.6.1, samtools 0.1.18, TrioCaller 0.1.1; we expect newer versions should also work. We assume all executables are i ...base quality 20 denotes 1% error probability and base quality 30 denotes 0.1% error probability). These error probabilities are each encoded in a single
  15 KB (2,470 words) - 18:01, 19 May 2015
• BaseQualityCheck
  ...s from the file. It may either be a text file with chr/index pairs, using 1-index position, one per line, or you may use a file created from mkgenomeve
  2 KB (372 words) - 04:35, 27 August 2010
• SeqShop: Sequence Mapping and Assembly Practical, May 2015
  wget https://github.com/statgen/gotcloud/archive/gotcloud.1.17.4.tar.gz tar xvf gotcloud.1.17.4.tar.gz
  16 KB (2,503 words) - 03:00, 28 January 2016
• SeqShop: Sequence Mapping and Assembly Practical, June 2014
  * One line per paired-end read (only 1 line per pair). cut -f 1,4 ${SS}/align.index
  16 KB (2,571 words) - 11:07, 2 February 2017
• Minimac3 ChangeLog
  ==Ver 2.0.1 (June 6, 2016)== Version : 2.0.1
  10 KB (1,262 words) - 22:24, 6 June 2016
• SeqShop: Calling Your Own Genome, December 2014
  The list of BAMs has already been created (just 1 BAM, your sample). The list of BAMs has already been created (just 1 BAM, your sample).
  18 KB (2,806 words) - 12:16, 15 December 2014
• Git FAQs
  {|border="1" git tag -a v1.1 -m 'version 1.1 contains the first version
  10 KB (1,582 words) - 18:50, 8 September 2015
• GREGOR
  Version : 1.1.0 ...ndow size. If you download r2 &ge; 0.7， you can define this number between 1 and 0.7.
  9 KB (1,222 words) - 17:39, 15 November 2016
• SeqShop: Sequence Mapping and Assembly Practical, December 2014
  wget https://github.com/statgen/gotcloud/archive/gotcloud.1.15.tar.gz tar xvf gotcloud.1.15.tar.gz
  17 KB (2,608 words) - 16:35, 15 May 2015

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