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

Hi,

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

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

perl fastq2fasta.pl 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
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