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  • bcftools consensus: shorter consensus sequences

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

  • #2
    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

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