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FrankiB

02-07-2014 07:30 AM

BWA -mem

Hi,

I'm using bwa-mem and how it is possible to know the percentage of reads mapped to the genome and all the stats?

GenoMax

02-07-2014 09:16 AM

Sort and index your bam file. Then you can use "samtools idxstats" / "samtools flagstat".

FrankiB

02-07-2014 09:31 AM

Quote:

Originally Posted by GenoMax (Post 131987)

Sort and index your bam file. Then you can use "samtools idxstats" / "samtools flagstat".

Ok I see, thank you

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