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  • 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

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