Hi all,
I've been working with bwa, maq and samtools for a few weeks now, and my PI just came across an unusual result which now has me worried about my results. I started off my workflow by running MAQ on a data set and matching against a restricted chromosomal region of hg18. I now have output with an example as follows:
HWUSI-EAS211R_5:2:6:90:1384 131 chr9_22054888_22134171 1 99 35M * 0 172 ATCCTTGGAGTTGTGAGGATTTAATGCAATTGTCT WWWWWWWWWWWWWWWWWVWWWWWWWUWWWVUUUUT MF:i:18 AM:i:99 SM:i:99 NM:i:1 UQ:i:30 H0:i:1 H1:i:0
My question is this: what is going on with the tags NM, H0 and H1 (in bold above). NM:i:1 should mean that the read has one mismatch to the genome, which seems to be true if I blat back to the reference. However H0:i:1 should mean that there is an exact match to the genome, and H1:i:1 should mean that there are no matches with distance 1 from the reference. Am I misinterpreting the tags or is this really inconsistent? If it is inconsistent, where is the bug (MAQ or maq2sam-long) and how can I fix it?
--Will
I've been working with bwa, maq and samtools for a few weeks now, and my PI just came across an unusual result which now has me worried about my results. I started off my workflow by running MAQ on a data set and matching against a restricted chromosomal region of hg18. I now have output with an example as follows:
HWUSI-EAS211R_5:2:6:90:1384 131 chr9_22054888_22134171 1 99 35M * 0 172 ATCCTTGGAGTTGTGAGGATTTAATGCAATTGTCT WWWWWWWWWWWWWWWWWVWWWWWWWUWWWVUUUUT MF:i:18 AM:i:99 SM:i:99 NM:i:1 UQ:i:30 H0:i:1 H1:i:0
My question is this: what is going on with the tags NM, H0 and H1 (in bold above). NM:i:1 should mean that the read has one mismatch to the genome, which seems to be true if I blat back to the reference. However H0:i:1 should mean that there is an exact match to the genome, and H1:i:1 should mean that there are no matches with distance 1 from the reference. Am I misinterpreting the tags or is this really inconsistent? If it is inconsistent, where is the bug (MAQ or maq2sam-long) and how can I fix it?
--Will
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