I was wondering if anyone has come across this before. Basically we’re getting SNPs that were identified using MAQ, and subsequently validated by Sanger sequencing, not being called by BWA/SAMTools on the same set of reads (same sequence.txt files) yet the BWA/SAMTools pileup shows that there is an alternate allele present at the SNP location.
In the example below, for both BWA and MAQ a similar number of reads mapped over the SNP (134 for BWA and 130 for MAQ). The SAMTools pileup shows that there is an alternate allele present (T), yet no SNP is called. I thought that MAQ’s SNP caller and the SAMtools SNP caller used the same algorithm so I’m confused as to why the SNP was not called by SAMTools. It is not being filtered out by varFilter as adding the –p flag doesn’t identify it either.
BWA + SAMtools pileup:
C C 73 0 58 134 ,$,$,$,$,$,$TT,,,T.A..,,,,.t,,,,,,.T.T.......,,,..........t............,........TTTT........tttttt........ttt,tt.............TTt,,t,,,,t,,,t
MAQ + MAQ’s SNP caller output:
C Y 37 130 1.00 63 62 C 250 T
MAQ Pileup:
C 130 @......TT...A,,,....,.....,T,,,,T,,,,...,,,,,,,,,,t,,,,,,,,,,,,.,,,,,,,,TTT,,,,,,,,tttttt,,,,,,,,tttt.t,,,,,,,,,,,,,TTt.....t...t.t
In the example below, for both BWA and MAQ a similar number of reads mapped over the SNP (134 for BWA and 130 for MAQ). The SAMTools pileup shows that there is an alternate allele present (T), yet no SNP is called. I thought that MAQ’s SNP caller and the SAMtools SNP caller used the same algorithm so I’m confused as to why the SNP was not called by SAMTools. It is not being filtered out by varFilter as adding the –p flag doesn’t identify it either.
BWA + SAMtools pileup:
C C 73 0 58 134 ,$,$,$,$,$,$TT,,,T.A..,,,,.t,,,,,,.T.T.......,,,..........t............,........TTTT........tttttt........ttt,tt.............TTt,,t,,,,t,,,t
MAQ + MAQ’s SNP caller output:
C Y 37 130 1.00 63 62 C 250 T
MAQ Pileup:
C 130 @......TT...A,,,....,.....,T,,,,T,,,,...,,,,,,,,,,t,,,,,,,,,,,,.,,,,,,,,TTT,,,,,,,,tttttt,,,,,,,,tttt.t,,,,,,,,,,,,,TTt.....t...t.t
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