Hi,
I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:
From PL value, P(D|TT)=10^(-2.7), P(D|TA)=0. So TA allele should be the most possible allele.
But in the processed vcf using this command:
This SNP is:
There is no alternative base information, but the AF1 is about 0.5, which means this is an heterozygous allele. And, if I use the following command, there is no SNP called at all.
Why the alternative base is not A??? Is there any option I can choose to call this SNP?
BTW, I am using samtools version 0.1.10-6.
Cheers,
Jun
I am using samtools/bcftools to call SNPs. I have a question on bcftools, I don't understand why this SNP is not called by bcftools. For example, this is the result of test.bcf file, which is created by:
Code:
samtools mpileup -ugf ref.fa seq.bam >test.bcf
chr21 8588396 . T A,X 0 . DP=13;I16=1,9,0,3,378,14392,73,1809,600,36000,180,10800,93,1075,42,642 PL 27,0,57,190,199,232
But in the processed vcf using this command:
Code:
bcftools view -c test.bcf > test_count.vcf
chr21 8588396 . T . 4.76 . DP=13;AF1=0.4995;CI95=0.5,0.5;DP4=1,9,0,3;MQ=60;PV4=1,5.9e-05,1,1 PL 27
Code:
bcftools view -vcg test.bcf > test_count.vcf
BTW, I am using samtools version 0.1.10-6.
Cheers,
Jun
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