Question: Problem about Getting Consensus Sequence Of Mapping Against Reference Genome Using Samtools Mpileup
gravatar for wangyang703092
4.4 years ago by
wangyang70309290 wrote:


I have a set of reads mapped against a reference genome and need take consensus sequence.So i used the pipeline ,I used the command:

samtools mpileup -uf <reference.fasta> <file.sorted.bam> | bcftools view -cg - | vcf2fq |

perl cns.fasta

In the vcf file,there actually exists indels, but in the final consensus sequence, there is no indels.

For example,in the vcf

Supercontig_1.1 2953301 .       T       TCGTGGCCT       178     .       INDEL;IS=2,0.014493;DP=138;VDB=2.191453e-01;AF1=1;AC1=2;DP4=0,0,75,55;MQ=20;FQ=-290     GT:PL:GQ        1/1:219,255,0:99

Someone have any suggestions?

samtools bcftools consensus • 1.7k views
ADD COMMENTlink written 4.4 years ago by wangyang70309290
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1555 users visited in the last hour