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create mutect pipeline #699

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
what sort of metrics would people be interested in. the only output is a vcf, 
but what can we pull back into ecdp

Original issue reported on code.google.com by zack...@gmail.com on 22 Mar 2014 at 5:16

GoogleCodeExporter commented 8 years ago 
testing pipeline. had to convert cosmic b37 to hg19 coords

errors when using java7

Original comment by zack...@gmail.com on 12 Apr 2014 at 4:37

GoogleCodeExporter commented 8 years ago 
usage: 

software/mutect/default/wrap_mutect.pl -t tumor1.bam -n normal1.bam -o myoutput 
-r /home/uec-00/shared/production/genomes/hg19_rCRSchrm/hg19_rCRSchrm.fa

will product myoutput.mutect_stats.txt and myoutput_coverage.wig

Original comment by zack...@gmail.com on 8 May 2014 at 10:53

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 20 May 2014 at 11:45

GoogleCodeExporter commented 8 years ago 
will add gatk indel realn and baseQ recalib

Original comment by zack...@gmail.com on 25 Jun 2014 at 8:48

GoogleCodeExporter commented 8 years ago 
indel realn and bsqr added

Original comment by zack...@gmail.com on 29 Jul 2014 at 10:24

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 12 Mar 2015 at 7:29