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FrankiB 02-07-2014 06:30 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 08:16 AM

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

FrankiB 02-07-2014 08:31 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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