Search results

• 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

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