Bioscope Hard Clip Vs Mismatch

Question

[Dave]

Does anyone know how bioscope decides to Hard Clip vs calling a mismatch ?

For eg :

1781_585_1567 0 validated 586867 54 34M1H * 0
0 ==================================
IIIIIIIIIIII:EI<FIIDDIIIIIII@EIIII RG:Z:20110112194907919
NH:i:1 CM:i:0 CQ:Z:<BBAB>A=B?BB4'?2+<@:+:@A@=</<%A4?>?
CS:Z:T11212021130133312020233301002211032 NM:i:0 MD:Z:34

Why is the above read are not classified as 35 bp read length with 1 mismatch?

Thanks!

Answer 1

[Pierre Lindenbaum]

I think it comes from the way the algorithm scores the pairwise alignment. "The hard clipping operation H indicates that the clipped sequence is not present in the sequence field"

It would be a mismatch if the whole sequence of the read was aligned on the reference. But here, for hard clipping, I guess the algorithm choose to end the pairwise alignment before the last base because the score for the alignment would be higher than the one with an extra gap.

[Dave]

That makes sense. Thanks Pierre!