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Strange. One suggestion...try
samtools mpileup -Buf my.fa my.bam | bcftools view -vcg
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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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Have you solved this problem? I also have this problem, and I'm very interested in the result.
Originally posted by grievous View PostHi 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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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, 10:46 AM.
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