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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
  • C++ Class: SamRecord
    [[Category:C++]] This class is part of [[C++ Library: libStatGen]].
    2 KB (237 words) - 11:02, 2 February 2017
  • Software
    [[Category:C++]] ...e of next generation sequencing and genotyping data, we have created these C++ library and tools that use that library.
    3 KB (469 words) - 17:20, 11 September 2021
  • Biostatistics 815 Term Project
    * A software package (C++ standalone or R/C++ combined package) containing source code, binary, and example data to tes * Input Data : Training and test data at http://www.kaggle.com/c/digit-recognizer
    4 KB (613 words) - 23:35, 19 September 2012
  • BamUtil: dumpAsp
    0:1010 DETAILED 1 C 6 0 0 0 0:1011 DETAILED 1 C > 1 0 0
    5 KB (646 words) - 17:39, 3 January 2014
  • BamUtil: trimBam
    ...g to '!' unless the optional parameter --clip/-c is specified. If --clip/-c is specified, the ends will be soft clipped instead of modified. == Soft Clipping Notes (--clip/-c) ==
    7 KB (1,105 words) - 23:28, 12 November 2017
  • RareMETALS
    cov.file <- c("study1.MetaCov.assoc.gz","study2.MetaCov.assoc.gz") score.stat.file <- c("study1.MetaScore.assoc.gz","study2.MetaScore.assoc.gz")
    18 KB (2,053 words) - 10:18, 18 May 2017
  • FastQ Validation Criteria
    The following validation criteria is used by [[C++ Class: FastQFile|FastQFile class]] and the [[fastQValidator|the FastQ Val * Base Only: A C T G N a c t g n
    3 KB (529 words) - 14:01, 7 September 2011
  • C++ Class: SamFileHeader
    [[Category:C++]] This class is part of [[C++ Library: libStatGen]].
    2 KB (322 words) - 11:05, 2 February 2017
  • Famrvtest
    2 1 0 0 1 1.0 1 34 A C A C A C A C A C 4 1 0 0 2 0.9 1 13 A C A C A C A C A C
    7 KB (1,065 words) - 10:34, 21 February 2017
  • Installing MinGW & MSYS on Windows
    #'''Destination Folder''' should be '''C:\MinGW''' #The Default Destination of '''C:\msys\1.0''' is fine, so click '''Next >'''
    6 KB (952 words) - 12:30, 18 January 2012
  • BamUtil: FAQ
    ...shErrorModel by default uses an unordered_map which is only found in C++11/C++0x. : The code attempts to automatically detect whether or not you have C++11/C++0x by checking if the gcc version > X4.3.0.
    4 KB (605 words) - 13:04, 23 September 2014
  • RareMETALS2
    cov.file <- c("example1.MetaCov.assoc.gz","example2.MetaCov.assoc.gz") score.stat.file <- c("example1.MetaScore.assoc.gz","example2.MetaScore.assoc.gz")
    13 KB (1,350 words) - 15:11, 29 June 2015
  • SAM/BAM Classes FAQs
    * A: Use [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Cigar::getQue These methods are found in [[C++ Class: SamFile]].
    2 KB (282 words) - 17:20, 11 September 2021
  • Triodenovo
    ...A/A" is the homozygous reference allele, "A/C" is the heterozygous, and "C/C" is the homozygous alternative allele, where the reference and alternative ...:DGQ:DP:PL C/C:7.52:100:15:0,44,255 C/C:7.52:100:16:0,44,255 C/T:7.52:100:16:100,0,199
    8 KB (1,165 words) - 18:19, 11 January 2023
  • BAM
    Our [[C++ Library: libStatGen|libStatGen]] library reads both SAM and BAM format fi
    731 bytes (119 words) - 23:16, 26 February 2013
  • Tutorial: Low Pass Sequence Analysis Answers
    * '''Q4: What is the genotype at this position? (T/T,C/T or C/C?) How many reads are covering this position? Is this consistent with the re 33514465 T C GT:GD:GQ:PL 1/1:3:10:117,9,0
    6 KB (849 words) - 04:10, 23 June 2016
  • Introduction to new students
    * R/C++/perl/python code snipplets / toy examples of various packages ..._GitHowTo.pdf PDF presentation]], [[https://statgen.sph.umich.edu/w/images/c/c4/GitCheatSheet.pdf Cheatsheet]]
    2 KB (304 words) - 21:39, 17 June 2014
  • BaseQualityCheck
    baseQualityCheck [-c max record count] [-q minimumMapQuality] [-r reference] [-s dbSNP file] [-v -c -> only process first (max record count) of alignment.
    2 KB (372 words) - 04:35, 27 August 2010
  • CheckVCF.py
    ...alleles or alternative alleles that are not composited of 'A', 'T', 'G', 'C', '.' alleles. <pre>MismatchRefBase 19:50578409:G-C/T
    4 KB (602 words) - 11:36, 2 February 2017
  • Vmatch
    11 85576113 B681435 C CT 11 85576113 B681435 C CT
    5 KB (649 words) - 17:11, 23 January 2012
  • Tutorial: RAREMETAL
    tabix -c "#" -s 1 -b 2 -e 2 STUDY1.QT1.singlevar.score.txt.gz tabix -c "#" -s 1 -b 2 -e 2 STUDY1.QT1.singlevar.cov.txt.gz
    7 KB (1,000 words) - 17:51, 16 March 2018
  • SeqShop: Ancestry On Your Own Genome, May 2015
    $LASER/laser -g $SSREF/HGDP/HGDP_938.geno -c $SSREF/HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k $LASER/laser -g $SSREF/HGDP/HGDP.633K.euro.geno -c $SSREF/HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K
    5 KB (733 words) - 14:57, 21 May 2015
  • Biostatistics 666: Modeling Recombination and Migration in the Coalescent
    Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ and Altshuler D (2005) Calibrating a coalescen
    889 bytes (123 words) - 06:20, 2 October 2017
  • Biostatistics 501: Main Page
    | Probability (Part C) | Confidence Interval (Part C)
    3 KB (506 words) - 16:10, 10 July 2015
  • Pileup
    4. REF : Reference base in the reference genome. A,C,T,G,N. c. MAPQ : quality score of the mapping for the contig, this is also
    3 KB (434 words) - 15:06, 3 April 2012
  • C++ Class: SamFile
    [[Category:C++]] This class is part of [[C++ Library: libStatGen|C++ Library: libStatGen]].
    4 KB (572 words) - 11:03, 2 February 2017
  • SeqShop: Ancestry On Your Own Genome, June 2014
    $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -M $LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.Euro.laser.seq -K
    3 KB (464 words) - 14:32, 13 November 2014
  • FASTA
    ...itate indexing. Nearly all programs that support FASTA format recognize A, C, T, G and N as valid characters in the sequence. Many also recognize IUPAC
    843 bytes (123 words) - 19:39, 23 March 2010
  • Biostatistics 615/815: Main Page
    ...nderstanding of computational aspects in implementing statistical methods. C++ language will be used throughout the course. * Optional Textbook : Stephen Prata, "C++ Primer Plus", Sixth Edition, Addison-Wesley, 2011
    8 KB (1,077 words) - 21:53, 18 December 2012
  • SeqShop: Ancestry On Your Own Genome, December 2014
    $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M $LASER/laser -g $HGDP/HGDP.633K.euro.geno -c $HGDP/HGDP.633K.euro.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k
    5 KB (821 words) - 12:43, 12 December 2014

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