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Old 02-07-2014, 06:30 AM   #1
FrankiB
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Default 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?
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Old 02-07-2014, 08:16 AM   #2
GenoMax
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Sort and index your bam file. Then you can use "samtools idxstats" / "samtools flagstat".
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Old 02-07-2014, 08:31 AM   #3
FrankiB
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Quote:
Originally Posted by GenoMax View Post
Sort and index your bam file. Then you can use "samtools idxstats" / "samtools flagstat".
Ok I see, thank you
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