Check a bam file if it was hard clipped?

Question

[R.T. Canterbury]

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?

[GenoMax]

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?

[Pierre Lindenbaum]

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

what is that -Y please ?

[R.T. Canterbury]

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."