bcftools consensus: shorter consensus sequences

[ireneirene]

Hi all,
I am trying to get the consensus sequences for chloroplast genomes using a reference. Here are my command lines:

~/samtools-1.3/samtools mpileup -Ou -f REF alnsorted.bam | bcftools call -mv -Oz -o 1aln_paired.vcf.gz 

tabix aln_paired.vcf.gz

cat REF | bcftools consensus aln_paired.vcf.gz > consensus_paired.fa

I am getting shorter consensus sequences, my reference is 159.295 bp long and for each constructed genome I get around 158.700 158.900 bp. I have checked the vcf file and there are a lot of deletions. Is this something that can happen or I am using some wrong settings in my codes?

thanks a lot in advance
Irene

[finswimmer]

Hello,

why you crossposted this here on seqanswer, if you already get an answer/guess in biostars.

If this answer isn't enough for you please give feedback there.

fin swimmer