Check a bam file if it was hard clipped?
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?
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GenoMax
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R.T. Canterbury •
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R.T. Canterbury •
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what is that
-Yplease ?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."
I guess you would not know that unless you compare to original reads.
How about checking CIGAR strings for
He.g.6H37M?