SAM flags could be improved?

[StevenWingett]

From Helen Ray-Jones:

We figured out what is going wrong with WASP. The problem is that the re-mapping step sometimes swaps the designation for read 1 and read 2, compared with the initial mapping.

Example:

In “to_remap.bam”:

A00551:155:HCYCKDSXY:3:1158:21097:31516 147 9 133332642 42 150M = 133348035 0 GCCTTCCTGGCCTTCTCTTTCGCCCACAGCTCCTTTCGCTTCCTCTTCTTCCGGTCCCGTTCCTGCTTTCTCCGCCGCCTTTTCTCCAAGGCGGCAGGGGACAGCTCCTTGGCACTGCCCTGGGGGAAAGAGGCACCCACTCATTAAAGT FFF:FFFFFFF:FFF,F:FFFFFFFFFFFFFF,F,FFFFFFFF:FFFFFFFFFF,FFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:25G124 YT:Z:UU CT:Z:FAR
A00551:155:HCYCKDSXY:3:1158:21097:31516 99 9 133348035 42 146M = 133332642 0 CCGCCGCAGTCTCTCTTCCCCGCCGCGCCGCGGTCCGAAAACCTAGTCAGCCGCCGCAGCCTCTCAGCCCCGCCTCGATTTTTAGCTTTATAGGAATGCTGTTGCTTTAAATCCGAAATCCCGTGCCGGTATCAACTCTCGCGATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF,FF:FFFFFFFFFFF AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:65G80 YT:Z:UU CT:Z:FAR

The first read at position ending 642 has FLAG 147 (“second in pair”) and the second read at position ending 035 has FLAG 99 (“first in pair”).

Then in “remapped.bam”:

A00551:155:HCYCKDSXY:3:1158:21097:31516.133332642-133348035.1.1 99 9 133332642 42 150M = 133348035 0 GCCTTCCTGGCCTTCTCTTTCGCCCGCAGCTCCTTTCGCTTCCTCTTCTTCCGGTCCCGTTCCTGCTTTCTCCGCCGCCTTTTCTCCAAGGCGGCAGGGGACAGCTCCTTGGCACTGCCCTGGGGGAAAGAGGCACCCACTCATTAAAGT FFF:FFFFFFF:FFF,F:FFFFFFFFFFFFFF,F,FFFFFFFF:FFFFFFFFFF,FFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:150 YT:Z:UU
A00551:155:HCYCKDSXY:3:1158:21097:31516.133332642-133348035.1.1 147 9 133348035 42 146M = 133332642 0 CCGCCGCAGTCTCTCTTCCCCGCCGCGCCGCGGTCCGAAAACCTAGTCAGCCGCCGCAGCCTCTCAGCCCCGCCTCGATTTTTAGCTTTATAGGAATGCTGTTGCTTTAAATCCGAAATCCCGTGCCGGTATCAACTCTCGCGATC FFFFFFFFFFF:FF,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:65G80 YT:Z:UU

The first read at position ending 642 now has FLAG 99 (“first in pair”) and the second read at position ending 035 has FLAG 147 (“second in pair”).

This is fine but means that WASP thinks that the cigars do not match up after remapping (even though they do in reality). So we can keep these reads that WASP is discarding.