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Old 06-19-2011, 09:58 AM   #1
grievous
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Location: Germany

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Default mpileup and homozygous snps

Hi all,

I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

whole command (samtools-0.1.16):
samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

Can anyone tell me the reason for this behaviour?
Thank you.

Last edited by grievous; 06-19-2011 at 10:46 AM.
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Old 03-03-2012, 06:36 PM   #2
idyll_ty
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Location: LA

Join Date: Nov 2011
Posts: 5
Default

Have you solved this problem? I also have this problem, and I'm very interested in the result.

Quote:
Originally Posted by grievous View Post
Hi all,

I'm new to SNP-calling with mpileup/bcftools. After my first analysis it seems to me, that I cannot properly call homozygous SNPs...

whole command (samtools-0.1.16):
samtools mpileup -uf my.fa my.bam | bcftools view -vcg -

1. output of mpileup (here in pileup-format, looks homozygous to me -> G?!):
chrX 2779570 A 41 GGGGGGGGGGGGGGgGgGGGGGGGGGgGGgGGGGgGGGGGg I<FHIIBEB?FIIIIEGGHIIIGHGDGIHDBIGIH=IIIH#

2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

Can anyone tell me the reason for this behaviour?
Thank you.
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Old 12-07-2012, 08:28 PM   #3
biomichael
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Location: China

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This is surely a heterozygos SNP site from A to G
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Old 02-19-2014, 04:54 AM   #4
maivantan
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Location: Vietnam

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2. output of bcftools (looks heterozygous to me):
chrX 2779570 . A G 99 . DP=41;AF1=0.5;CI95=0.5,0.5;DP4=0,0,35,5;MQ=60 PL:GT:GQ 255,120,255:0/1:99

I think this is heterozygous SNP, you can see this values 0/1:99
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Old 02-19-2014, 08:32 AM   #5
swbarnes2
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Posts: 912
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Strange. One suggestion...try

Quote:
samtools mpileup -Buf my.fa my.bam | bcftools view -vcg
The -B turns off BAQ recalculation..I've gotten strange results when it was on, which were repaired by turning it off.
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Old 02-19-2014, 04:58 PM   #6
Jeremy
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Location: Pathum Thani, Thailand

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You could try a different SNP calling program like freebayes or gatk.
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