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I have a very large bam file and I want to filter it to keep only a handfull of positions as defined in a bed file. Can I do this with sambamba or do i need another tool?

Thanks

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Jun 6, 2022 at 10:55

2 Answers 2

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I think it is possible:

sambamba view --regions regions.bed --with-header --format=bam reads.bam  > filtered.bam
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  • $\begingroup$ Hi @Pablo could you kindly edit your question inserting this as a suggestion? $\endgroup$
    – M__
    Commented Jun 6, 2022 at 19:17
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You need bedtools, specifically bedtools intersect command, not sambamba:

bedtools intersect -abam A.bam -b B.bed > A_in_N.bam
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