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Why am I getting two values of AF1 from mpileup? Heisman Bioinformatics 0 12-29-2011 12:58 PM

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Old 09-26-2011, 01:42 AM   #1
liying
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Default How samtools computes AF1?

Hi,Sorry to ask basic.

I get such vcf by smtools mpileup, But can't understand it.

scaffold_1 8463589 . T C 47 . DP=5;VDB=0.0520;AF1=0.500;AFE=0.500;DP4=0,0,3,2;MQ=38 PL:GT:GQ 92,15,92:0/1:77

The ref is T, all my 5 reads are C at this site. So how the AF1 (site allele frequency of the strongest non-reference allele) is 0.5 ?
How samtools computes AF1?

PS: I didn't find any explain about AFE. what is it?

Thanks!
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Old 09-26-2011, 06:12 PM   #2
liying
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It turns out be a version error. We didn't change $PATH of bcftools when updata samtools.
Now the result is

scaffold_1 8463589 . T C 59.3 . DP=5;VDB=0.0520;AF1=1;AC1=2;DP4=0,0,3,2;MQ=38;FQ=-42 GT:PL:GQ 1/1:92,15,0:27

AF1 look like alright. But what are VDB and AC1? I didn't find them in samtools, mpileup and VCF document.
I'm using samtools 0.1.18. Are them some new in this version?
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Old 09-26-2011, 08:29 PM   #3
Heisman
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Both of those are described (briefly) in the header section of the SNP files that are generated.

##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">

##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
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Old 09-26-2011, 09:03 PM   #4
liying
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Heisman,thank you very much!
My vcf file don't have any header. Could you post you command?

My command:
samtools mpileup -A -q 20 -Q 13 -C 50 -uf Egrandis_162.fa 2.rmdup.bam | bcftools view -bvcg - >2.RawVar.bcf 2>mpileup.log
bcftools view 2.RawVar.bcf | vcfutils.pl varFilter -Q 30 -d 2 - > 2.d2Q30.FilterVar.vcf
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Old 09-26-2011, 09:07 PM   #5
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samtools-0.1.18/samtools mpileup -AB -ugf [Reference_Sequence] [aligned_file] | samtools-0.1.18/bcftools/bcftools view -bvcg -> [Intermediate_File] &

samtools-0.1.18/bcftools/bcftools view [Intermediate_File] | samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > [Variant_Output] &
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Old 09-26-2011, 09:13 PM   #6
liying
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Heisman,thanks!

why use -g and -u together? We used piping, so it should be -u.

samtools mpileup
-g Compute genotype likelihoods and output them in the binary call format (BCF).
-u Similar to -g except that the output is uncompressed BCF, which is preferred for piping.

Well,I can't see why my file missing header.

Last edited by liying; 09-26-2011 at 10:13 PM.
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Old 04-13-2012, 06:15 AM   #7
jy123
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Hi,

I have a problem to understand the following result:
chr4 114612702 . G A 52 . DP=29;VDB=0.0218;AF1=1;AC1=8;DP4=6,4,10,9

How come that AF1=1 with ref and alt reads number having no big difference?
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