Question: samtools SNP calling
0
gravatar for evelyn
4 months ago by
evelyn30
evelyn30 wrote:

I am using samtools for SNP calling from .sorted.bam file:

bcftools mpileup -f ref.fa bwa.sorted.bam | bcftools view -Ov - > bwa.bcftools.vcf

VCF file gives REF calling but does not give ALT calling: A view from vcd file:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  bwa.sorted.bam
EL1.0ch00   23812   .   A   <*> 0   .   DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0  PL  0,0,0

Any suggestions will be helpful.

snp • 245 views
ADD COMMENTlink modified 4 months ago by Kevin Blighe50k • written 4 months ago by evelyn30
2

The <*> has a meaning - see here: What does <*> mean in a vcf file?

You should be piping mpileup into bcftools call, by the way - see here: A: Genotyping with samtools/bcftools

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe50k
2
gravatar for finswimmer
4 months ago by
finswimmer12k
Germany
finswimmer12k wrote:

Hello evelyn ,

variant calling using bcftools is a 2-step process:

  1. First check each position of the reference if it contains a potential variant, using bcftools mpileup
  2. In a second step have a closer look at the positions that have potential variants and check more criteria, using bcftools call

The second step is missing in your case.

So a complete command line could look like this:

$ bcftools mpileup -Ou -f ref.fa aln.bam | bcftools call -mv -o output.vcf

fin swimmer

ADD COMMENTlink written 4 months ago by finswimmer12k

It worked, thanks!!!

ADD REPLYlink written 4 months ago by evelyn30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1790 users visited in the last hour