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samtools flagstat only for exome coordinates

Hi all,

Does anybody know if it s possible to obtain the samtools flagstat stats only for the exome coordinates?

Thank you in advance!

next-gen sequencing alignment
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by 2nelly 2nelly

1 answer 

samtools view -bu -L capture.bed in.bam |samtools  flagstat -
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you so much Pierre!

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written by 2nelly 2nelly

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