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change workflow to calc picard aln metrics on mdups #653

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
create new metric for pcr dups derived from this picard data:

PCR_Dups (RNASeq) = dups / total 

(this will exclude non-primary)

Original issue reported on code.google.com by zack...@gmail.com on 15 Jan 2014 at 8:38

GoogleCodeExporter commented 8 years ago 
Created a parser for  uniquely_mapped and uniquely_mapped_duplicates
metrics. Those metrics are coming from a  picard alignment metrics file
.*hg19_rCRSchrm.fa.mdups.bam.rfNumberHitsEqualsOne.FlagStat.metric.txt
generated by Zack.

Original comment by natalia....@gmail.com on 22 Jan 2014 at 12:42

GoogleCodeExporter commented 8 years ago

Original comment by zack...@gmail.com on 12 Feb 2014 at 10:57