Filter bam file based on cigar string?
How can I filter a bam file using samtools view that retains reads where the cigar string contains M<=35?
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Ruoshui •
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bioinf_sci •
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bioinf_sci •
2 answers
A bit messy, but it can be done with regexp matching:
samtools view -e 'cigar =~ "(^|[^0-9])([0-9]|[12][0-9]|3[0-5])M"' -o out.bam in.bam
The regexp is start or non-digit, followed by ?M [12]?M or 3[012345]M.
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jkbonfield
using samjdk: https://jvarkit.readthedocs.io/en/latest/SamJdk/
I cannot post code here ! there is a bug ni biostars...
so here is a gist:
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Pierre Lindenbaum
java -jar src/jvarkit-git/dist/jvarkit.jar samjdk -e 'return !record.getReadUnmappedFlag() && record.getCigar().getCigarElements().stream().filter(CE->CE.getOperator().equals(CigarOperator.M)).anyMatch(CE->CE.getLength()<=45);' in.bam
Posting code here in case gist goes away.
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