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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
  • LibStatGen: GLF
    [[Category:C++]]
    1 KB (214 words) - 11:01, 2 February 2017
  • Screen Commands
    | Create New Window || Ctrl-a c
    1 KB (193 words) - 12:44, 6 February 2015
  • Verifying Sample Identities - Implementation
    c) Evaluate this log-sum assuming <math>P_{ibd} = 0.5</math>. This assumes we ...rgest. Sequencing a parent or offspring of the target sample will maximize c). Sequencing a completely incorrect sample will maximize b).
    4 KB (741 words) - 10:25, 29 April 2010
  • CalcMatch
    CalcMatch is a C/C++ software developed by [https://csg.sph.umich.edu//yli/ Yun Li]. It compar (C) freq1: major allele frequency
    5 KB (686 words) - 12:03, 2 February 2017
  • 830 - MarkovModel::Impute()
    char labels[] = {0, 'a', 'c', 'g', 't'};
    1 KB (165 words) - 14:50, 25 September 2013
  • Relationship between Ploidy, Alleles and Genotypes
    <span style="color:#FF0000">C</span>DD <br> ...demonstrated in the following table to obtain the index of the genotype C/C/D.
    11 KB (1,773 words) - 21:07, 18 October 2017
  • SAM
    If you are writing software to read SAM or BAM data, our C++ [[C++ Library: libStatGen|libStatGen]] is a good resource to use. Reference: C C A T A C T G A A C T G A C T A A C
    12 KB (2,011 words) - 16:10, 11 September 2015
  • BamGenotypeCheck
    -c [int] ''stop after reading [int] filtered sequence reads'' -C [int] ''stop after reading [int] reads, filtered or not''
    3 KB (521 words) - 11:11, 2 February 2017
  • 830 - MINIMAC::main()
    "(c) 2010-2011 Goncalo Abecasis, Christian Fuchsberger\n"); ifprintf(haps, "%s%c", j % 8 == 0 ? " " : "", mm.imputedAlleles[j]);
    12 KB (1,088 words) - 15:06, 2 October 2013
  • GlfTrio
    glfTrio -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \ -c ''genotype likelihood file'' Child's [[GLF]]-format genotype likelihood
    4 KB (470 words) - 12:45, 1 May 2012
  • Minimac Command Reference
    ...ts "1", "2", "3", "4" are also acceptable and treated as aliases for "A", "C", "G", "T".
    4 KB (576 words) - 03:40, 28 January 2015
  • Code Sample: Generating Manhattan Plots in R
    col=c("gray","darkgray"), panel.extra=NULL, pch=20, cex=0.8,...) { posshift <- head(c(0,cumsum(posmax)),-1);
    19 KB (3,167 words) - 10:49, 14 January 2014
  • C++ Library: general Change Log
    * Update [[C++ Class: InputFile|'''InputFile''']] * Update [[C++ Class: InputFile|'''InputFile''']]
    5 KB (769 words) - 12:57, 1 May 2012
  • RAREMETAL FAQ
    make -C ../../libStatGen --no-print-directory opt ...ABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c
    7 KB (1,054 words) - 11:46, 20 March 2018
  • Ancestry
    Ancestry is implemented in C++ for fast computations. 1 1005806 rs3934834 C T
    4 KB (566 words) - 14:53, 12 August 2014
  • Arf
    #-c option directs the output to STDOUT arf -a complexity 1000g.vcf -g genome.fa -l 30 -c
    4 KB (663 words) - 18:38, 2 February 2012
  • VcfCodingSnps
    To Compile the source code, please first re-compile the .c functions in the library folder on your local machine: ...". Type syntax "gcc -c -O2 *.cpp -D_FILE_OFFSET_BITS=32" to re-compile the c files in the library if use a 32-bit local machine
    14 KB (1,768 words) - 11:58, 2 February 2017
  • FastQValidator
    [[Category:C++]] ...complete. It was built using [[LibStatGen: FASTQ]] which is part of the [[C++ Library: libStatGen|libStatGen]] library.
    11 KB (1,458 words) - 11:00, 2 February 2017
  • Tutorial: EMMAX GotCloud STOM: Lecture 2
    cut -c 96- ~/out/naive.assoc.linear | Rscript $S2/r/calc.GC.lambda.r grep -w ADD ~/out/pca.assoc.linear | cut -c 96- | Rscript $S2/r/calc.GC.lambda.r
    4 KB (623 words) - 03:07, 6 January 2014
  • CSG Tech Talks
    * [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]
    2 KB (277 words) - 13:56, 23 August 2017
  • PileupBasedVariantCalling
    1 10469 C 5 .g,$,. A?/;P >>>FF 78,66,100,38,12 1 10471 C 4 .,,. D=:Q >>FF 80,68,40,14
    7 KB (1,018 words) - 15:52, 10 September 2013
  • Base Caller Summaries
    **C channel illumination overlaps with A: a C label fluoresces in A channel (similarly G and T overlap) Kao, W.-C., Stevens, K., Song, Y.S. (2009) BayesCall: A model-based base-calling algo
    6 KB (910 words) - 17:04, 12 March 2010
  • MaCH: machX
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
    2 KB (293 words) - 12:02, 2 February 2017
  • Thunder
    ...under example/thunder/ folder, input files extracted from real data and a C-shell script that executes the whole analysis pipeline. Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR. Low-coverage sequencing: Implications for
    4 KB (605 words) - 12:08, 21 February 2017
  • Mach DAC
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
    2 KB (321 words) - 11:24, 2 February 2017
  • Summary Statistics Files Specification for RAREMETAL and rvtests
    1 762320 C T 5916 0.00635386 0.00388776 46 1 1... 1 564766 T C 2659 0.23223 1235 1 0 2041 1 617 20.54
    8 KB (658 words) - 11:39, 29 August 2019
  • LASER
    LASER, which stands for Locating Ancestry using SEquencing Reads, is a C++ software package that can estimate individual ancestry directly from geno ./laser -s pileup2seq/test.seq -g resource/HGDP/HGDP_938.geno -c resource/HGDP/HGDP_938.RefPC.coord -o test -k 2
    12 KB (1,605 words) - 11:51, 2 February 2017
  • Trial Enrichment
    Copyright (c) 2013, Hyun Min Kang <hmkang@umich.edu> and Youna Hu
    2 KB (322 words) - 18:28, 21 May 2013
  • C++ Library: libStatGen
    [[Category:C++]] Open source, freely available (GPL license), easy to use C++ APIs
    11 KB (1,679 words) - 17:21, 11 September 2021
  • Haploxt
    haploxt is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li] and [ht
    4 KB (510 words) - 18:22, 21 October 2010
  • M3VCF Files
    6 89921 chr6:89921 C T . . B1.M3;R=2;A=4 0000 6 100116 chr6:100116 C A . . B1.M6;R=2;A=1 0001
    6 KB (799 words) - 20:35, 29 January 2015
  • Class Notes
    ...s related to modern statistical computing. Most of the examples will be in C++ and a prior introduction to statistics and computing is recommended.
    2 KB (247 words) - 16:44, 4 February 2015
  • Biostatistics 615/815 Fall 2011
    ...ing of computational aspects in implementing statistical methods. Although C++ language will be used throughout the course, using Java programming langu === Part I : C++ Basics and Introductory Algorithms ===
    11 KB (1,312 words) - 17:35, 31 August 2012
  • LiftOver
    10000199 A/G 7 4589694 4589694 2 3 C - 7 4623168 4623168 2 3 C - 10000199 A/G 12 57008620 57008620 2 3 C - 12 58722353 58722353 2 3 C -
    14 KB (2,263 words) - 18:33, 15 July 2015
  • RAREMETAL Documentation
    tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.score.txt.gz tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz
    24 KB (3,256 words) - 13:22, 20 May 2019
  • Biostatistics 830 - Code Snippets
    Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype impu
    2 KB (214 words) - 13:53, 28 October 2013
  • TabAnno
    ...put.vcf -o output.vcf -r hs37d5.fa -g refFlat_hg19.txt.gz -p priority.txt -c codon.txt -c : Specify codon file (default: codon.txt)
    14 KB (1,969 words) - 11:57, 2 February 2017
  • SEQMIX
    '''SEQMIX''' is a C++ program that takes advantage of off-targeted sequence reads from exome/ta
    2 KB (373 words) - 03:07, 4 November 2013
  • VICES
    -c, --contam-threshold <float> Threshold for estimating donor samples * G. J. M. Zajac, L. G. Fritsche, S. L. Dagenais, R. H. Lyons, C. M. Brummett, & G. Abecasis. ''VICES: Verify Intensity Contamination from E
    6 KB (787 words) - 09:59, 15 April 2019
  • Tandem Repeat Concepts
    C 20:131948:C/CCA
    8 KB (798 words) - 19:17, 25 February 2016
  • C++ Class: InputFile
    [[Category:C++]]
    2 KB (406 words) - 10:47, 2 February 2017
  • RAREMETALWORKER
    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
    18 KB (2,478 words) - 13:34, 20 November 2019
  • LibStatGen: ASP
    [[Category:C++]] | refBase || Reference Base || 4 bits || 0=A, 1=C, 2=G, 3=T, 4=N
    19 KB (2,589 words) - 11:45, 30 April 2012
  • MaCH FAQ
    awk '{print $'''3'''}' orig.hap | cut -c${first}-${last} &gt; region.hap zcat orig.hap.gz | awk '{print $'''3'''}' | cut -c${first}-${last} &gt; region.hap
    13 KB (2,030 words) - 11:22, 2 February 2017
  • Biostatistics 830: Main Page
    ...Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, * Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype impu
    7 KB (1,068 words) - 03:43, 5 January 2017
  • BamUtil
    [[Category:C++]] ** Update to add compile option to compile without C++0x/C++11
    17 KB (2,168 words) - 17:14, 11 September 2021
  • StarCluster
    #* <pre>starcluster start -c gccluster mycluster</pre> #* <pre>starcluster start -c gccluster mycluster</pre>
    14 KB (2,139 words) - 10:49, 7 November 2014
  • Minimac2
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). :::: FAM1003 ID1234 0 0 M A/A A/A C/C
    13 KB (2,050 words) - 12:53, 9 March 2018
  • BamUtil: validate
    ...ion is not set. A description of the statistics generated are found at: [[C++ Class: SamFile#Statistic Generation|Sam File Statistics]] FAIL_PARSE: Invalid Tag Format: *, should be cc:c:x*.
    7 KB (990 words) - 14:05, 6 January 2014
  • BamUtil: filter
    ...a match if the reference and the read have the same base (both A/a, both C/c, both G/g, or both T/t). If they are different, non-'N', bases it is a mis
    10 KB (1,546 words) - 14:07, 6 January 2014
  • Bayesdenovo
    1 118 . C A 100 . AF=0.333333;AC=7;DP=1629;FDQ=8.667414 GT:DQ 1 858 . C A 100 . AF=0.333333;AC=10;DP=1592;FDQ=8.688325 GT:DQ
    6 KB (900 words) - 10:22, 26 October 2016
  • Variant Call Pipeline
    Configuration file cna be specified with -c option. If -c not specified, will be read file "seq_pipeline.conf"
    7 KB (907 words) - 15:36, 21 December 2010
  • C++ Class: FastQFile
    [[Category:C++]]
    4 KB (529 words) - 10:58, 2 February 2017
  • SeqShop: Genetic Association Analysis Practical, June 2014
    -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/ -c [/home/hmkang/seqshop/epacts/share/EPACTS/codon.txt]
    19 KB (2,551 words) - 10:27, 2 February 2017
  • RareSimu
    Genetic Model-based Simulator [GMS] is an efficient c++ program for simulating case control data sets based on genetic models. Th
    2 KB (365 words) - 11:11, 2 February 2017
  • SeqShop: Association Analysis, May 2015
    -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/ -c [/home/hmkang/seqshop/epacts/share/EPACTS/codon.txt]
    20 KB (2,538 words) - 14:15, 21 May 2015
  • GlfSingle
    *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account f
    3 KB (404 words) - 11:34, 26 September 2013
  • LibStatGen Download
    See [[C++ Library: libStatGen]]. For information about obtaining the latest Development Versions, see [[C++ Library: libStatGen#Where to Find It|Where to Find libStatGen]]
    10 KB (1,430 words) - 00:04, 13 November 2017
  • Variant classification
    ALT C #SNP, 1 tv ...tv, note that we get the SNP after truncating the bases ATTT to reveal a G/C transversion SNP
    15 KB (1,324 words) - 21:44, 25 February 2016
  • RAREFY COMMAND
    ...adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file).
    3 KB (482 words) - 05:09, 17 February 2015
  • GotCloud: FAQs
    ...VERSION not defined; tview is NOT compiled"</nowiki><br />bam_tview_curses.c<nowiki>:287:2: warning: #warning "No curses library is available; tview wit ...i><br /><nowiki>/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616: note: std::string std::to
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  • Examples of Read Mapping with Karma and BWA
    # A,C,G,T,N in every line of color space sequence and omitting the bwa index -a bwtsw -p bwa.ref/ncbi.color.ref -c \
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  • SeqShop: Genetic Association Analysis Practical, December 2014
    -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/ -c [/home/hmkang/seqshop/epacts/share/EPACTS/codon.txt]
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  • Tutorial: Low Pass Sequence Analysis
    ...h C and 2 read with T (equal to the reference) the most likely genotype is C/T indicated as Y (according to [http://www.bioinformatics.org/sms2/iupac.ht Note: The total count of C is 4, but 2 of them are duplicates. Similarly the number of T is 2 but one
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  • Biostatistics 866: Main Page
    ...Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, * Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype impu
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  • SplitPed
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
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  • MutationFilter
    1 10000 10000 A C 11 190324 190324 A C INDEL,AB,BQM 0 5 0 2:3:0:0 0 1 0
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  • Minimac
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). :::: FAM1003 ID1234 0 0 M A/A A/A C/C
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  • METAL Documentation
    ...xample, when one study provides A/G alleles and a different study provides C/T alleles). ...a,c,g,t) and can be on either strand if not an A/T or C/G SNP. For A/T or C/G SNPs, METAL requires SNPs to be on a consistent strand in different input
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  • SeqShop: Calling Your Own Genome, May 2015
    ...at $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6 --out run ...T/vcfs/chrX/chrX.filtered.rsid.anno.exon.vcf.gz | grep -v ^#) | $HK/bgzip -c > $OUT/wgs.filtered.rsid.anno.exon.vcf.gz
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  • GREGOR
    ...= -E/tmp -i -m2000 -j10,11,12,13,14,15,16,17,18,19,120,122,123,124,125 sh -c ...mosix, this parameter can be "-E/tmp -i -m2000 -j10,11,12,13,14,15,16 sh -c"; when you define "slurm", it can be "--partition=1000g --time=0:30:0"
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  • Debuggers
    ***:<pre>ulimit -c unlimited</pre>
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  • Code Sample: Generating QQ Plots in R
    exp.x<-c() qqunif.plot(my.pvalue.list, auto.key=list(corner=c(.95,.05)))
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  • EMMAX
    If one wants to adjust for covariates simultanenously, add -c [cov_file] options to the above run, with the covariate file similar to the Kang HM, Sul JH, Service SK, Zaitlen NA, Kong SY, Freimer NB, Sabatti C, Eskin E. (2010) Variance component model to account for sample structure i
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  • Minimac: 1000 Genomes Imputation Cookbook
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele). :::: FAM1003 ID1234 0 0 M A/A A/A C/C
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  • SeqShop: Estimates of Genetic Ancestry Practical, May 2015
    $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapm $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapm
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  • SeqShop: Calling Your Own Genome, December 2014
    Ctrl-c ...at $OUT/vcfs/chr1/chr1.filtered.rsid.anno.vcf.gz | grep Exon;)| $HK/bgzip -c > $OUT/vcfs/chr1/chr1.filtered.rsid.anno.exon.vcf.gz" --numjobs 6
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  • MEAGA
    [http://www.ncbi.nlm.nih.gov/pubmed/25480373 Lam C. Tsoi, James T. Elder, Gonçalo R. Abecasis. (2015) Graphical algorithm fo ...u have any questions, please contact [[mailto:tsoi.teen@gmail.com Alex Lam C Tsoi]].
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  • Polymutt2
    Li B, Wei Q, Zhan X, Zhong X, Chen W, Li C, et al. (2015) Leveraging Identity-by-Descent for Accurate Genotype Inferen
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  • EPACTS for DIAGRAM
    C AGE</pre> Key: &nbsp;A =&nbsp;binary trait; T = quantitative trait; C = covariate<br>
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  • SeqShop: Estimates of Genetic Ancestry Practical, June 2014
    ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapm ./LASER-2.01/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapm
    10 KB (1,458 words) - 10:23, 2 February 2017
  • RvTests
    ...eighted method) are implemented in the logisitc regression framework using C++. Please contact Youna Hu (youna@umich.edu) for comments, suggestions or q
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  • METAL Quick Start
    | c | c
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  • Understanding vcf-summary output
    ...(Ts or Ti) refers to the bi-allelic SNPs where two alleles are A <-> G or C <-> T. In true SNPs, transitions more frequently occurs than transversions.
    5 KB (800 words) - 22:31, 23 November 2014
  • SeqShop: Estimates of Genetic Ancestry Practical, December 2014
    $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 1 -y 3 -o hapm $LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s hapmap_trios.seq -K 20 -k 4 -x 4 -y 6 -o hapm
    10 KB (1,511 words) - 10:24, 2 February 2017
  • Make file tutorial
    GNU Make is often thought of as a tool for managing the compilation of large C programs. This is true, but its potential is not limited to this! for my $c (@cmd)
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  • Sam Library Usage Examples
    This page contains examples on how to use the [[C++ Library: libStatGen|SAM/BAM Library]].
    11 KB (1,206 words) - 09:07, 7 September 2011
  • Rare variant tests
    | C-alpha || [Neale et al., submitted] ||
    7 KB (933 words) - 11:35, 2 February 2017
  • MaCH: 1000 Genomes Imputation Cookbook
    ...Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
    6 KB (896 words) - 03:08, 28 July 2011
  • Biostatistics 830: Fall 2013 Edition
    ...Crosby J, Hixson JE, Rea TJ, Muzny DM, Lewis LR, Wheeler DA, Sabo A, Lusk C, Weiss KG, Akbar H, Cree A, Hawes AC, Newsham I, Varghese RT, Villasana D, * Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype impu
    8 KB (1,143 words) - 13:59, 2 September 2014
  • TrioCaller
    ...h is ~3x. README.txt describes the structure of the package. Pipeline.csh (C shell) and pipeline.bash (bash shell) are two scripts for you to run all co For c shell
    15 KB (2,470 words) - 18:01, 19 May 2015
  • SeqShop: Variant Calling and Filtering for SNPs Practical, May 2015
    <li><code>36907001</code>; Ref: T, Alt: C - that's what we saw before</li> <li><code>36907098</code>; Ref: T, Alt: C - that's what we saw before</li>
    19 KB (2,813 words) - 18:35, 19 August 2015
  • SeqShop: Variant Calling and Filtering for SNPs Practical, December 2014
    <li><code>36907001</code>; Ref: T, Alt: C - that's what we saw before</li> <li><code>36907098</code>; Ref: T, Alt: C - that's what we saw before</li>
    19 KB (2,942 words) - 19:12, 30 March 2015
  • SeqShop: Variant Calling and Filtering for SNPs Practical, June 2014
    <li><code>36907001</code>; Ref: T, Alt: C - that's what we saw before</li> <li><code>36907098</code>; Ref: T, Alt: C - that's what we saw before</li>
    20 KB (2,959 words) - 14:37, 13 November 2014
  • DosageConvertor
    DosageConvertor is a C++ tool to convert dosage files (in VCF format) from [[Minimac4| Minimac3/4]
    8 KB (1,151 words) - 14:01, 18 January 2019
  • Rvtests
    ...ot;#&quot; $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c &gt; $your_vcf_file ...include or exclude the IDs in the file.<br />So to include sample A, B and C, you can provide a file, <code>people.txt</code>, looks like:
    29 KB (4,420 words) - 00:31, 12 May 2016
  • Minimac3
    ''Das S, Forer L, Schönherr S, Sidore C, Locke AE'' et al. Next-generation genotype imputation service and methods.
    7 KB (1,080 words) - 15:40, 18 October 2022
  • Minimac: Tutorial
    Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.
    7 KB (1,087 words) - 12:34, 25 January 2017
  • VerifyBamID
    20 61651 SNP20-9651 C A . PASS CR=99.86851;GentrainScore=0.7055;HW=0.077647716;AN=2180;AC=11 20 63244 rs6139074 A C . PASS CR=98.893394;GentrainScore=0.8001;HW=7.327299E-7;AN=2162;AC=501
    20 KB (2,795 words) - 15:29, 9 September 2017
  • Tutorial: GotCloud UW CMG
    -c [/home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/ ...session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/hg19_gencodeV14.txt.gz -c /home/presenter02/day2/session1/uwcmg_2013_08/epacts/bin/..//share/EPACTS/c
    46 KB (5,757 words) - 16:15, 6 August 2013
  • SAM Validation Criteria
    [[C++ Library: libbam|BamFile]]
    11 KB (1,444 words) - 15:51, 27 August 2010
  • GLF
    ...// 0..15 => XACMGRSVTWYHKDBN, so that 0x01 = A, 0x02 = C, 0x04 = G, 0x08 = T
    8 KB (1,103 words) - 11:22, 13 August 2013
  • Vt
    #run make, note that compilers need to support the c++0x standard Some features of C++11 are used, thus there is a need for newer versions of gcc and clang.
    81 KB (9,677 words) - 04:36, 4 May 2021
  • Biostatistics 615/815 Winter 2011
    ...ing of computational aspects in implementing statistical methods. Although C++ language will be used throughout the course, using Java programming langu * Lecture 2 : C++ Basics and Precisions -- [[Media:Biostat615-lecture2-handout-nup.pdf | (H
    36 KB (4,875 words) - 00:10, 6 September 2011
  • EPACTS
    ** Core input/output routines are implemented in C++ 20 60479 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.894;LDAF=0.0020;AVGPOST
    41 KB (5,647 words) - 08:03, 19 February 2019
  • SeqShop: Aligning Your Own Genome, June 2014
    Copy (Ctrl-c) your table from EXCEL (including the header row, but with no extra rows/co
    11 KB (1,960 words) - 14:25, 13 November 2014
  • Variant Normalization
    ...an A nucleotide on the left side of the variant's alleles and truncate the C on the right side of the variant's alleles. It is however parsimonious. </
    15 KB (2,331 words) - 09:55, 1 August 2016
  • 1000 Genomes Project Pilot 1 SNP Calling
    Notes:<br>(1) Cleaned monomorphic sites before feeding to thunder (no need, b/c thunder 005 handles AL1/-)<br>(2) All sites are bi-allelic with one of the
    7 KB (1,088 words) - 13:35, 10 March 2010
  • Exome Chip Design
    ...ped on the Illumina Omni 2.5M array were favored and markers with A/T or G/C alleles were avoided. ...ped on the Illumina Omni 2.5M array were favored and markers with A/T or G/C alleles were avoided.
    21 KB (2,877 words) - 07:42, 6 August 2013
  • LibStatGen: VCF
    [[Category:C++]]
    18 KB (2,634 words) - 16:09, 23 January 2013
  • Creating an AMI on EC2
    history -c
    11 KB (1,759 words) - 14:54, 14 October 2014
  • SardiNIA
    ...M, Scuteri A, Orru M, Albai G, Dei M, Lai S, Usala G, Lai M, Loi P, Mameli C, Vacca L, Deiana M, Olla N, Masala M, Cao A, Najjar SS, Terracciano A, Nedo
    12 KB (1,693 words) - 10:24, 8 September 2018
  • GotCloud: Binary Releases
    dpkg-buildpackage: export C...
    15 KB (2,137 words) - 23:29, 7 January 2016
  • Generic Exome Analysis Plan
    : Calculate the proportion of A, C, G, T bases along each read. Flag runs with evidence of unusual patterns of
    11 KB (1,630 words) - 13:07, 21 May 2010
  • Polymutt
    -c : minimum cutoff of posterior probability to output a variant [''Default: 0
    13 KB (2,106 words) - 10:12, 27 April 2014
  • SeqShop: Analysis of Structural Variation Practical, June 2014
    grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c
    17 KB (2,452 words) - 14:37, 13 November 2014
  • Karma
    -c Creates a color space reference and index/hash
    14 KB (2,190 words) - 11:10, 2 February 2017
  • SeqShop: Analysis of Structural Variation Practical, May 2015
    grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c
    20 KB (2,783 words) - 15:56, 25 August 2015
  • SeqShop: Analysis of Structural Variation Practical, December 2014
    grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c
    21 KB (2,922 words) - 17:09, 17 December 2014
  • LocusZoom Standalone
    | 1 || 30967 || 30970 || 1:30967_CCCA/C || 2657 || 435.35 || 1 || 0.081925 || 0.08848 || -1.7035 || 1326 || 1331 ||
    45 KB (6,829 words) - 18:03, 18 November 2021
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