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Old 10-19-2010, 04:12 PM   #1
Location: Melbourne

Join Date: Jan 2010
Posts: 21
Default MAQ vs BWA/SAMTools - differences in SNP calling algorithm?

I was wondering if anyone has come across this before. Basically were 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 MAQs SNP caller and the SAMtools SNP caller used the same algorithm so Im confused as to why the SNP was not called by SAMTools. It is not being filtered out by varFilter as adding the p flag doesnt 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 + MAQs 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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Old 10-20-2010, 06:26 AM   #2
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Location: USA, Midwest

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Did you run varFilter after samtools pileup? The varFilter has a maximum read depth cutoff parameter for SNP calling (-D). The default value is 100. With a read depth of 134 the SNP would be rejected.
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Old 10-20-2010, 03:17 PM   #3
Location: Melbourne

Join Date: Jan 2010
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Thanks for the suggestion but I ran varFilter with a read depth cutoff of 1,000,000 so that can't be the reason. Also I ran varFilter with the -p option aswell which prints the SNPs that are filtered out by varFilter and that SNP does not make it into that file either.
So for some reason it's not getting recognised as a SNP by SAMTools yet MAQ was able to call it.
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