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- 37 bytes (3 words) - 01:53, 2 November 2010
- [[Category:C++]]4 KB (529 words) - 10:58, 2 February 2017
- // Name of the first allele, typically "A", "C", "G" or "T" for SNPs2 KB (241 words) - 16:37, 13 April 2010
- 26 bytes (2 words) - 17:28, 7 March 2011
- [[Category:C++]]2 KB (406 words) - 10:47, 2 February 2017
- The Savvy C++ library is an Interface to various variant calling formats, most notably156 bytes (24 words) - 15:50, 19 April 2018
- [[Category:C++]] See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Betwe5 KB (712 words) - 12:00, 2 February 2017
- 28 bytes (2 words) - 13:26, 2 June 2010
- 17 bytes (2 words) - 13:28, 2 June 2010
- [[Category:C++]] This class is part of [[C++ Library: libStatGen]].2 KB (237 words) - 11:02, 2 February 2017
- 2 KB (169 words) - 12:27, 2 August 2010
- [[Category:C++]] This class is part of [[C++ Library: libStatGen]].2 KB (322 words) - 11:05, 2 February 2017
- 33 bytes (3 words) - 11:42, 25 October 2010
- #REDIRECT [[C++ Library: libbam]]33 bytes (4 words) - 17:19, 6 April 2010
- 35 bytes (3 words) - 11:47, 25 October 2010
- [[Category:C++]] This class is part of [[C++ Library: libStatGen|C++ Library: libStatGen]].4 KB (572 words) - 11:03, 2 February 2017
- [[Category:C++]] Open source, freely available (GPL license), easy to use C++ APIs11 KB (1,679 words) - 17:21, 11 September 2021
- * Update [[C++ Class: InputFile|'''InputFile''']] * Update [[C++ Class: InputFile|'''InputFile''']]5 KB (769 words) - 12:57, 1 May 2012
- #REDIRECT [[C++ Library: general Change Log]]45 bytes (6 words) - 01:55, 2 November 2010
- #REDIRECT [[C++ Library: FASTQ Change Log]]43 bytes (6 words) - 01:17, 2 November 2010
- 3 KB (380 words) - 12:56, 1 May 2012
Page text matches
- ...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 C649 bytes (96 words) - 10:24, 4 June 2010
- * [[C++ Library: libStatGen]] - C++ library for working with Genetic Data Files * [[BamUtil]] - command-line (C++) tools for working with SAM/BAM files448 bytes (67 words) - 14:52, 17 June 2013
- ...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
- #REDIRECT [[Savvy C++ Library]]31 bytes (4 words) - 15:50, 19 April 2018
- 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 algo964 bytes (131 words) - 11:42, 26 February 2010
- '''The contents of this page have been merged into [[C++ Library: libStatGen]]'''81 bytes (13 words) - 15:24, 23 August 2011
- c = fd[6] # print 'c=', c2 KB (287 words) - 11:33, 10 August 2011
- [[Category:C++]] See [[C++ Class: CigarRoller#Mapping Between Reference and Read/Query|Mapping Betwe5 KB (712 words) - 12:00, 2 February 2017
- [[Category:C++]] The fastQ Library is now a part of [[C++ Library: libStatGen]].2 KB (345 words) - 10:49, 2 February 2017
- [[Category:C++]] See [[C++ Library: libStatGen]] for more descirption on the library.2 KB (223 words) - 10:51, 2 February 2017
- The Savvy C++ library is an Interface to various variant calling formats, most notably156 bytes (24 words) - 15:50, 19 April 2018
- ...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>''' T4 KB (434 words) - 17:25, 21 September 2010
- [[Category:C++]] These executables are built using [[C++ Library: libStatGen]].1 KB (149 words) - 13:06, 9 September 2011
- 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
- *[[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 app2 KB (306 words) - 20:29, 16 February 2015
- ...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
- colvec=c(1,2); pchvec=c(1,2);3 KB (299 words) - 10:03, 23 October 2014
- 1 20 1:20 G C 1 30 1:30 C A3 KB (398 words) - 17:01, 19 February 2013
- ...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 C7 KB (1,251 words) - 11:31, 2 February 2017
- [[Category:C++]] | <code>[[C++ Class: SamFile|SamFile]]</code>4 KB (566 words) - 10:55, 2 February 2017
- [[Category:C++]] This class is part of [[C++ Library: libStatGen]].2 KB (237 words) - 11:02, 2 February 2017
- [[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
- * 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-recognizer4 KB (613 words) - 23:35, 19 September 2012
- 0:1010 DETAILED 1 C 6 0 0 0 0:1011 DETAILED 1 C > 1 0 05 KB (646 words) - 17:39, 3 January 2014
- ...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
- 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
- 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 n3 KB (529 words) - 14:01, 7 September 2011
- [[Category:C++]] This class is part of [[C++ Library: libStatGen]].2 KB (322 words) - 11:05, 2 February 2017
- 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 C7 KB (1,065 words) - 10:34, 21 February 2017
- #'''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
- ...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
- 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
- * 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
- ...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:7.52:100:16:100,0,1998 KB (1,165 words) - 18:19, 11 January 2023
- Our [[C++ Library: libStatGen|libStatGen]] library reads both SAM and BAM format fi731 bytes (119 words) - 23:16, 26 February 2013
- * '''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 1/1:3:10:117,9,06 KB (849 words) - 04:10, 23 June 2016
- * 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 [-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
- ...alleles or alternative alleles that are not composited of 'A', 'T', 'G', 'C', '.' alleles. <pre>MismatchRefBase 19:50578409:G-C/T4 KB (602 words) - 11:36, 2 February 2017
- 11 85576113 B681435 C CT 11 85576113 B681435 C CT5 KB (649 words) - 17:11, 23 January 2012
- 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.gz7 KB (1,000 words) - 17:51, 16 March 2018
- $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 -K5 KB (733 words) - 14:57, 21 May 2015
- Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ and Altshuler D (2005) Calibrating a coalescen889 bytes (123 words) - 06:20, 2 October 2017
- | Probability (Part C) | Confidence Interval (Part C)3 KB (506 words) - 16:10, 10 July 2015
- 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 also3 KB (434 words) - 15:06, 3 April 2012
- [[Category:C++]] This class is part of [[C++ Library: libStatGen|C++ Library: libStatGen]].4 KB (572 words) - 11:03, 2 February 2017
- $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 -K3 KB (464 words) - 14:32, 13 November 2014
- ...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 IUPAC843 bytes (123 words) - 19:39, 23 March 2010
- ...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, 20118 KB (1,077 words) - 21:53, 18 December 2012
- $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 -k5 KB (821 words) - 12:43, 12 December 2014
- [[Category:C++]]1 KB (214 words) - 11:01, 2 February 2017
- | Create New Window || Ctrl-a c1 KB (193 words) - 12:44, 6 February 2015
- 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 is a C/C++ software developed by [https://csg.sph.umich.edu//yli/ Yun Li]. It compar (C) freq1: major allele frequency5 KB (686 words) - 12:03, 2 February 2017
- char labels[] = {0, 'a', 'c', 'g', 't'};1 KB (165 words) - 14:50, 25 September 2013
- <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
- 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 C12 KB (2,011 words) - 16:10, 11 September 2015
- -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
- "(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 -f NA19239.chrom20.SLX.glf -m NA19238.chrom20.SLX.glf -c NA19240.chrom20.SLX.glf \ -c ''genotype likelihood file'' Child's [[GLF]]-format genotype likelihood4 KB (470 words) - 12:45, 1 May 2012
- ...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
- 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
- * Update [[C++ Class: InputFile|'''InputFile''']] * Update [[C++ Class: InputFile|'''InputFile''']]5 KB (769 words) - 12:57, 1 May 2012
- make -C ../../libStatGen --no-print-directory opt ...ABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c7 KB (1,054 words) - 11:46, 20 March 2018
- Ancestry is implemented in C++ for fast computations. 1 1005806 rs3934834 C T4 KB (566 words) - 14:53, 12 August 2014
- #-c option directs the output to STDOUT arf -a complexity 1000g.vcf -g genome.fa -l 30 -c4 KB (663 words) - 18:38, 2 February 2012
- 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 machine14 KB (1,768 words) - 11:58, 2 February 2017
- [[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
- 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 $S2/r/calc.GC.lambda.r4 KB (623 words) - 03:07, 6 January 2014
- * [[Media:Cplusplus11-features-and-tricks.pdf| C++11 Features and Tricks by Daniel Taliun (Jul 28, 2016)]]2 KB (277 words) - 13:56, 23 August 2017
- 1 10469 C 5 .g,$,. A?/;P >>>FF 78,66,100,38,12 1 10471 C 4 .,,. D=:Q >>FF 80,68,40,147 KB (1,018 words) - 15:52, 10 September 2013
- **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 algo6 KB (910 words) - 17:04, 12 March 2010
- ...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
- ...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 for4 KB (605 words) - 12:08, 21 February 2017
- ...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
- 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 20.548 KB (658 words) - 11:39, 29 August 2019
- 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 212 KB (1,605 words) - 11:51, 2 February 2017
- Copyright (c) 2013, Hyun Min Kang <hmkang@umich.edu> and Youna Hu2 KB (322 words) - 18:28, 21 May 2013
- [[Category:C++]] Open source, freely available (GPL license), easy to use C++ APIs11 KB (1,679 words) - 17:21, 11 September 2021
- haploxt is a C/C++ software developed by [https://www.sph.umich.edu/csg/yli/ Yun Li] and [ht4 KB (510 words) - 18:22, 21 October 2010
- 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 00016 KB (799 words) - 20:35, 29 January 2015
- ...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
- ...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
- 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
- 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.gz24 KB (3,256 words) - 13:22, 20 May 2019
- Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype impu2 KB (214 words) - 13:53, 28 October 2013
- ...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''' is a C++ program that takes advantage of off-targeted sequence reads from exome/ta2 KB (373 words) - 03:07, 4 November 2013
- -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 E6 KB (787 words) - 09:59, 15 April 2019
- C 20:131948:C/CCA8 KB (798 words) - 19:17, 25 February 2016
- [[Category:C++]]2 KB (406 words) - 10:47, 2 February 2017
- 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 C18 KB (2,478 words) - 13:34, 20 November 2019
- [[Category:C++]] | refBase || Reference Base || 4 bits || 0=A, 1=C, 2=G, 3=T, 4=N19 KB (2,589 words) - 11:45, 30 April 2012
- awk '{print $'''3'''}' orig.hap | cut -c${first}-${last} > region.hap zcat orig.hap.gz | awk '{print $'''3'''}' | cut -c${first}-${last} > region.hap13 KB (2,030 words) - 11:22, 2 February 2017
- ...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 impu7 KB (1,068 words) - 03:43, 5 January 2017
- [[Category:C++]] ** Update to add compile option to compile without C++0x/C++1117 KB (2,168 words) - 17:14, 11 September 2021
- #* <pre>starcluster start -c gccluster mycluster</pre> #* <pre>starcluster start -c gccluster mycluster</pre>14 KB (2,139 words) - 10:49, 7 November 2014
- ...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/C13 KB (2,050 words) - 12:53, 9 March 2018
- ...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
- ...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 mis10 KB (1,546 words) - 14:07, 6 January 2014
- 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:DQ6 KB (900 words) - 10:22, 26 October 2016
- 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
- [[Category:C++]]4 KB (529 words) - 10:58, 2 February 2017
- -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
- Genetic Model-based Simulator [GMS] is an efficient c++ program for simulating case control data sets based on genetic models. Th2 KB (365 words) - 11:11, 2 February 2017
- -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
- *Mutation model: Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account f3 KB (404 words) - 11:34, 26 September 2013
- 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
- ALT C #SNP, 1 tv ...tv, note that we get the SNP after truncating the bases ATTT to reveal a G/C transversion SNP15 KB (1,324 words) - 21:44, 25 February 2016
- ...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
- ...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::to12 KB (1,871 words) - 10:54, 23 June 2015
- # 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 \11 KB (1,700 words) - 16:50, 23 September 2014
- -c /home/hmkang/seqshop/epacts/share/EPACTS/codon.txt -o /net/seqshop-server/ -c [/home/hmkang/seqshop/epacts/share/EPACTS/codon.txt]21 KB (2,694 words) - 10:27, 2 February 2017
- ...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 one18 KB (2,867 words) - 03:59, 17 September 2019
- ...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 impu9 KB (1,319 words) - 07:21, 18 April 2017
- ...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).4 KB (538 words) - 11:33, 2 February 2017
- 1 10000 10000 A C 11 190324 190324 A C INDEL,AB,BQM 0 5 0 2:3:0:0 0 1 08 KB (1,107 words) - 01:06, 16 April 2013
- ...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/C16 KB (2,442 words) - 12:53, 9 March 2018
- ...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 input19 KB (2,912 words) - 15:52, 22 December 2017
- ...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.gz13 KB (2,110 words) - 12:10, 22 May 2015
- ...= -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"9 KB (1,222 words) - 17:39, 15 November 2016
- ***:<pre>ulimit -c unlimited</pre>4 KB (606 words) - 14:33, 23 September 2014
- exp.x<-c() qqunif.plot(my.pvalue.list, auto.key=list(corner=c(.95,.05)))9 KB (1,398 words) - 14:14, 12 November 2013
- 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 i7 KB (989 words) - 09:58, 2 February 2017
- ...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/C19 KB (2,860 words) - 03:40, 28 January 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 hapm8 KB (1,248 words) - 09:57, 2 February 2017
- 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 618 KB (2,806 words) - 12:16, 15 December 2014
- [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]].9 KB (1,307 words) - 21:37, 4 March 2015
- Li B, Wei Q, Zhan X, Zhong X, Chen W, Li C, et al. (2015) Leveraging Identity-by-Descent for Accurate Genotype Inferen4 KB (623 words) - 23:54, 10 November 2016
- C AGE</pre> Key: A = binary trait; T = quantitative trait; C = covariate<br>24 KB (3,442 words) - 10:05, 2 February 2017
- ./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 hapm10 KB (1,458 words) - 10:23, 2 February 2017
- ...eighted method) are implemented in the logisitc regression framework using C++. Please contact Youna Hu (youna@umich.edu) for comments, suggestions or q4 KB (623 words) - 22:59, 13 January 2015
- | c | c18 KB (2,804 words) - 13:11, 5 April 2010
- ...(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
- $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 hapm10 KB (1,511 words) - 10:24, 2 February 2017
- 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)44 KB (6,347 words) - 21:00, 14 July 2021
- 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
- | C-alpha || [Neale et al., submitted] ||7 KB (933 words) - 11:35, 2 February 2017
- ...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
- ...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 impu8 KB (1,143 words) - 13:59, 2 September 2014
- ...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 shell15 KB (2,470 words) - 18:01, 19 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
- <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
- <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 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
- ...ot;#" $your_old_vcf | sed 's:^chr::ig' | sort -k1,1n -k2,2n) | bgzip -c > $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
- ''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
- Howie B, Fuchsberger C, Stephens M, Marchini J, and Abecasis GR.7 KB (1,087 words) - 12:34, 25 January 2017
- 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=50120 KB (2,795 words) - 15:29, 9 September 2017
- -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/c46 KB (5,757 words) - 16:15, 6 August 2013
- [[C++ Library: libbam|BamFile]]11 KB (1,444 words) - 15:51, 27 August 2010
- ...// 0..15 => XACMGRSVTWYHKDBN, so that 0x01 = A, 0x02 = C, 0x04 = G, 0x08 = T8 KB (1,103 words) - 11:22, 13 August 2013
- #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
- ...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 | (H36 KB (4,875 words) - 00:10, 6 September 2011
- ** 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;AVGPOST41 KB (5,647 words) - 08:03, 19 February 2019
- Copy (Ctrl-c) your table from EXCEL (including the header row, but with no extra rows/co11 KB (1,960 words) - 14:25, 13 November 2014
- ...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
- 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 the7 KB (1,088 words) - 13:35, 10 March 2010
- ...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
- [[Category:C++]]18 KB (2,634 words) - 16:09, 23 January 2013
- history -c11 KB (1,759 words) - 14:54, 14 October 2014
- ...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, Nedo12 KB (1,693 words) - 10:24, 8 September 2018
- dpkg-buildpackage: export C...15 KB (2,137 words) - 23:29, 7 January 2016
- : Calculate the proportion of A, C, G, T bases along each read. Flag runs with evidence of unusual patterns of11 KB (1,630 words) - 13:07, 21 May 2010
- -c : minimum cutoff of posterior probability to output a variant [''Default: 013 KB (2,106 words) - 10:12, 27 April 2014
- grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c17 KB (2,452 words) - 14:37, 13 November 2014
- -c Creates a color space reference and index/hash14 KB (2,190 words) - 11:10, 2 February 2017
- grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c20 KB (2,783 words) - 15:56, 25 August 2015
- grep -v ^# $OUT/sv/discovery/discovery.vcf | cut -f 7 | sort | uniq -c21 KB (2,922 words) - 17:09, 17 December 2014
- | 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