Check a bam file if it was hard clipped?

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4.5 years ago

R.T. Canterbury ▴ 10

Is there a programmatic way to verify that a BAM file was hard clipped? The BAM file header does not show the -Y was used. Does this require manual verification in IGV?

Hardclipping BAM IGV • 1.4k views

ADD COMMENT • link updated 4.5 years ago by GenoMax 154k • written 4.5 years ago by R.T. Canterbury ▴ 10

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Does this require manual verification in IGV?

I guess you would not know that unless you compare to original reads.

How about checking CIGAR strings for H e.g. 6H37M?

ADD REPLY • link 4.5 years ago by GenoMax 154k

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The BAM file header does not show the -Y was used

what is that -Y please ?

ADD REPLY • link 4.5 years ago by Pierre Lindenbaum 166k

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From bwa site (https://www.mankier.com/1/bwa)

"-Y Use soft clipping CIGAR operation for supplementary alignments. By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments."

ADD REPLY • link 4.5 years ago by R.T. Canterbury ▴ 10

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