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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

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