User:Lindenb/Notebook/UMR915/2012/03/02
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DailyExomeCNVhttp://cran.r-project.org/web/packages/ExomeCNV/index.html doc: https://secure.genome.ucla.edu/index.php/ExomeCNV_User_Guide install: mkdir lib > source("http://bioconductor.org/biocLite.R") > biocLite("DNAcopy",lib="lib") > .libPaths("lib") > library("ExomeCNV",lib="lib") Loading required package: DNAcopy ************************************************************************** The data format for the CNA object will be changed in version 1.23.0 Instead of a data frame it will be a list of 3 (or more) objects chrom and maploc will be vectors and CN/LOH data will be a matrix ************************************************************************** and http://genome.ucla.edu/~fah/ExomeCNV/script/makeCoverageScript.tar.gz liftover hg18->hg19 : baitlibrary_information/Agilent_sanger_exome_0809_PCCR.bed
$ file src/bam2coverage.sh src/bam2coverage.sh: gzip compressed data, from Unix, last modified: Thu Mar 1 23:49:58 2012 I mailed the author.
GATK and read groupshttps://getsatisfaction.com/gsa/topics/the_unified_genotyper_complains_about_a_missing_read_group Duplicate in BAMs$ ~/package/samtools-0.1.18/samtools view -F 4 -q 10 CD5121/CD5121_sorted.bam | awk -F ' ' '($3=="chr1" && $4=="3600741" && $8=="3600736")' HTKZQN1_353:3:1204:6076:118387 145 chr1 3600741 254 100M = 3600736 -105 CGCTGGACTGGTCAGCTGCTCGGCCCCGCCCACAGGCTGGCTGCCCCGCCCCGCCTCCGCCGCCCAGGGATTCGTAGGTGGGGAATTTGTTTGCGCTGCG ######################@BB@BB@<+48(<(88?0;58DB<5@B@<8?BB8@>8EIIIGHHEGIGGIGHDIGHEGGGHFEGIGHFHGFFDDD@@B BC:Z:0 XD:Z:9C90 SM:i:403 AS:i:0 HWI-ST980_147:6:2107:5294:13481 83 chr1 3600741 254 100M = 3600736 -105 CGCTGGCCTCGTCAGCTGCTCGCCCCCGCCCACGCGCTGGCTGCCCTGCCCCGCCTCCGCCGCCCAGGGATTCGTAGGTGGGGAATTTGATTGCGCTGCG ######################################?@@?<:0)&5-0-5?578;;9AIDIHF9HEHF?:)C<FEFEEBEHF?HEF?FFDD@DDB@@@ BC:Z:0 XD:Z:6A15G10AG11C42T10 SM:i:275 AS:i:637
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