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Old 03-15-2011, 09:41 AM   #1
wwmm933
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Default samtools pileup output, base quality does not match original ones

I found samtools pileup results show '!' in the base quality column. However, I think the lowest one should be #, right? Actually, the base qualities do not match original ones. Does anyone know why?

Base qualities in the input sam file have been changed to Sanger format before samtools pileup.

By the way, should we change the original base quality scores to Sanger quality format before BWA mapping?

Thanks!
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Old 11-30-2011, 08:29 AM   #2
Donby
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Quote:
Originally Posted by wwmm933 View Post
I found samtools pileup results show '!' in the base quality column. However, I think the lowest one should be #, right? Actually, the base qualities do not match original ones. Does anyone know why?

Base qualities in the input sam file have been changed to Sanger format before samtools pileup.

By the way, should we change the original base quality scores to Sanger quality format before BWA mapping?

Thanks!
I found the same problem yet!

Does someone knows?
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Old 11-30-2011, 08:42 AM   #3
swbarnes2
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Simple thing to try...try running mpileup with -B. The BAQ calcautions seomtimes wrongly diagnose SNPs as misaligned indels, and it'll change the base qualities.
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Old 11-30-2011, 09:52 PM   #4
Donby
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Originally Posted by swbarnes2 View Post
Simple thing to try...try running mpileup with -B. The BAQ calcautions seomtimes wrongly diagnose SNPs as misaligned indels, and it'll change the base qualities.
Thank you for your reply!
I know. It's another quality system after BAQ.

But now i want to use the BAQ and another problem came across that the mpileup of samtools-0.1.16 and samtools-0.1.18 gives different pileup results for a single data:

samtools-0.1.18 mpileup -q 1 -r chr1:12944616-12944616 -f hg19.fa merge.bam
chr1 12944616 T 51 A,,,aaa..,aaA,aa,aan,..A,.a.AAa..A,Aa.,....,A.,,,,. !^aa!#!a]a!!!a!!a!!Baaa!aa!Z!!!aa!a!!aaaaaaY!aYaaaa

samtools-0.1.16 mpileup -q 1 -r chr1:12944616-12944616 -f hg19.fa merge.bam
chr1 12944616 T 51 A,,,aaa..,aaA,aa,aan,..A,.a.AAa..A,Aa.,....,A.,,,,. bdfef\ff]fffXfffff_BdfeeddfZfbeffffbffeffcfYafYdedd

I don't know which gives the right result. Should i use samtools-0.1.18 for it is the latest version?
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