I have amplicon data that I want to align with BWA - I set the softclipping penalty very high (
-L 50) to force bwa to align end-to-end rather than soft-clipping in the middle of the read.
Now I have a read pair that is identical in R1 and R2, but I cannot make the aligner output the same alignments for both:
M06706:14:000000000-CN3FL:1:1110:20686:16364 99 xxx 12 43 72M22D2M20D36M = 12 72 ATGATGGGCTCTTCCCCCGCGTGCAGCAGTGGAGCCACCAGCAGCGGGTGGGCGACCTCTTCCAGAAGCTGGCAATTCGGCCATCACGGCTCTCCTCCAGTGGGACTCCC M06706:14:000000000-CN3FL:1:1110:20686:16364 147 xxx 12 45 72M38S = 12 -72 ATGATGGGCTCTTCCCCCGCGTGCAGCAGTGGAGCCACCAGCAGCGGGTGGGCGACCTCTTCCAGAAGCTGGCAATTCGGCCATCACGGCTCTCCTCCAGTGGGACTCCC
There should be two long deletions in the read - as shown in the first one. But in the second, it prefers to soft-clip no matter what I do. I have tried everything, raising the soft-clip penalty even higher, changing match, gap open, gap extension penalties. But no matter what I do, I cannot change the
I assume it has to do with the deletions being closer to the start of the second read, but shouldn't the high soft-clip penality force an alignment?
Any help how I can properly align from both directions would be very much appreciated!