Separate BAM reads by the number and type of mismatchs on the read
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2 days ago
Anna-Leigh • 0

I want to split an aligned RNA-seq into 2 files, every read with more than one mismatch of a given type (every T>C mutation) into one sam/bam, and the others into another sam/bam.

I'm sure I could do it with pysamtools, but was wondering if there is an easier way by directly parsing the MD tag. Could probably get partially there with a quick filter on the NM tag, but I also want specific types of mismatches.

bam pysamtools rna-seq samtools • 34 views

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