Problem about Getting Consensus Sequence Of Mapping Against Reference Genome Using Samtools Mpileup

Question

[wangyang703092]

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?