Question: Mpileup SNP calling
gravatar for d.angra
2.9 years ago by
United Kingdom
d.angra50 wrote:


I have used SAMtools Version=1.2+htslib-1.2.1 for SNP calling (History option 66 in Trinity 2). The output which I have obtained is something which I am unable to understand, I have used SAMtools older version which gave me output very different from what I have obtained. Can you please help me in this direction

My questions are

1) Why is the QUAL for all samples 0??

2) Why is the column on alternate allele with X.

3) How do I filter the output in the form of  SGB??


Looking forward for your help.






samtools • 1.1k views
ADD COMMENTlink written 2.9 years ago by d.angra50

In early version of  bcftools, "bcftools view" is used to call variants. In bcftools v1.2, "bcftools call" is used. You may want confirm correct command line is used.

ADD REPLYlink written 2.9 years ago by liangjiao.xue10
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