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how can i filter a sam file from a paf file

I used minimap2 to produce an alignment and I outputted it into 2 formats, .paf and .sam. I did some filtering on the .paf version and now I would like to filter the alignments in the .sam file the same way. How can I use the filtered .paf file to filter the .sam file so that only the same alignments exist in each file?

paf sam filter
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updated by ATpoint ATpoint • written by Mark • Mark

Just save yourself a lot of pain and learn to filter the sam/bam file efficiently. It is much more of a widespread standard than PAF.

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written by colindaven colindaven

1 answer

A quick search shows that paf2sam doesn't exist because a .paf file doesn't contain the CIGAR strings that .sam files have. A work around could be to convert your .paf to a bed file using splice2bed then use the bedtools suite such as bedtools intersect to limit your .bam file.

What are your end goals with this .sam file?

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written by Trivas • Trivas

samtools view can be used to limit a bam file for intervals in a BED via random access / the index, that is way more efficient than using intersect which goes through the entire file.

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written by ATpoint ATpoint

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