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  • MaCH: Pedigree with Integer Allele Codes
    ...des in pedigree 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 A A A C C C
    649 bytes (96 words) - 10:24, 4 June 2010
  • Mary Kate Wing
    * [[C++ Library: libStatGen]] - C++ library for working with Genetic Data Files * [[BamUtil]] - command-line (C++) tools for working with SAM/BAM files
    448 bytes (67 words) - 14:52, 17 June 2013
  • SNP Call Set Properties
    ...twice as frequently as transversions (changes from A <-> C, A <-> T, G <-> C or G <-> T). Thus, another useful diagnostic is the ratio of transitions to ...ns is that C->T changes (C reference, T variant) are more frequent than T->C changes. Likewise, G->A changes are more frequent than A->G changes.
    3 KB (529 words) - 19:08, 10 September 2012
  • Savvy
    #REDIRECT [[Savvy C++ Library]]
    31 bytes (4 words) - 15:50, 19 April 2018
  • Links to Sequence Analysis Tools
    Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I., Naef, F. (2008) Probabilistic base calling o Kao, W.-C., Stevens, K., Song, Y.S. (2009) BayesCall: A model-based base-calling algo
    964 bytes (131 words) - 11:42, 26 February 2010
  • LibStatGen Repository
    '''The contents of this page have been merged into [[C++ Library: libStatGen]]'''
    81 bytes (13 words) - 15:24, 23 August 2011
  • LiftRsNumber.py
    c = fd[6] # print 'c=', c
    2 KB (287 words) - 11:33, 10 August 2011
  • C++ Class: CigarRoller
    [[Category:C++]] See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Betwe
    5 KB (712 words) - 12:00, 2 February 2017
  • LibStatGen: FASTQ
    [[Category:C++]] The fastQ Library is now a part of [[C++ Library: libStatGen]].
    2 KB (345 words) - 10:49, 2 February 2017
  • LibStatGen: general
    [[Category:C++]] See [[C++ Library: libStatGen]] for more descirption on the library.
    2 KB (223 words) - 10:51, 2 February 2017
  • Savvy C++ Library
    The Savvy C++ library is an Interface to various variant calling formats, most notably
    156 bytes (24 words) - 15:50, 19 April 2018
  • SAM: Filtering Reads
    ...G A A C C T T G G A A A C T G C C G G G G A C T ...T T T A C T G A C T G A A A C C A '''<span style="color:red">T</span>''' T
    4 KB (434 words) - 17:25, 21 September 2010
  • StatgenTools
    [[Category:C++]] These executables are built using [[C++ Library: libStatGen]].
    1 KB (149 words) - 13:06, 9 September 2011
  • SAV File Format
    Accompanying the SAV format is the [[Savvy C++ Library | Savvy C++ programming library ]] for interfacing with it and other file formats. Th * [[Savvy C++ Library | Savvy]] (C++)
    2 KB (276 words) - 10:03, 22 May 2018
  • Shuang Feng
    *[[Rarefy|'''RAREFY''']] is a C++ tool to facilitate sequencing study design using family samples by select *[[Famrvtest|'''famrvtest''']] is an efficient C++ tool for rare variant association analysis using a linear-mixed model app
    2 KB (306 words) - 20:29, 16 February 2015
  • MaCH Options
    ...ing pedigree and reference together. Notice that it will not affect A/T or C/G SNPs as strand mismatch won't lead to more than two alleles.
    640 bytes (104 words) - 22:35, 28 June 2010
  • Understanding QPLOT output
    colvec=c(1,2); pchvec=c(1,2);
    3 KB (299 words) - 10:03, 23 October 2014
  • Vcf2geno
    1 20 1:20 G C 1 30 1:30 C A
    3 KB (398 words) - 17:01, 19 February 2013
  • MaCH: Input Files
    ...analysis tools, it is also possible to encode allels as 1 (for A), 2 (for C), 3 (for G) and 4 (for T). See below for an example: FAM1001 ID1234 0 0 M A A A C C C
    7 KB (1,251 words) - 11:31, 2 February 2017
  • LibStatGen: BAM
    [[Category:C++]] | <code>[[C++ Class: SamFile|SamFile]]</code>
    4 KB (566 words) - 10:55, 2 February 2017

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