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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

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