Consensus from mpileup error

Question

[mks002]

Dear all,

I am trying to generate the consensus sequence for whole genome sequencing. The reference has 11 segments.

The issue is when i am seeing the consensus output, the indels are not incorporated i.e for the insertion the bases should be added at that particular position and deleted in the other case. Only the SNPs are showing up properly in consensus.

So why indels are coming or what should be done to get it correctly done.

   samtools-0.1.18/samtools mpileup -E -uf reference.fna sorted.bam | samtools-0.1.18/bcftools/bcftools view -cg - | samtools-0.1.18/bcftools/vcfutils.pl vcf2fq > cns.fastq

seqtk seq -a cns.fastq > cns.fasta

One more query is that the start 1-3 position of the consensus is also changed, which i checked in the mpileup is same as reference without and SNPs or indels. why is this issue coming.

What would be the possible way to do this. Awaiting for kind replies .:)