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Old 05-05-2017, 08:06 AM   #1
MattRSmith
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Location: US

Join Date: May 2017
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Default Variant calling: reference positions with no reads don't appear in vcf file

Hello,

I mapped my reads back to a reference genome using BWA-mem and now I'm using the bcftools mpileup/call/filter pipeline to obtain variant calls. I was converting my vcf files to fasta sequences for each of my individuals, masking non-called and filtered sites (./.) with Ns. However, I noticed that reference positions to where no reads where mapped in the original bam do not appear in any of my bcf or vcf files. For example, in my chromosome 1, since no reads mapped from position 1 to 100, my vcf file will start in position 1:100, and not 1:1. Therefore, when I use bcftools consensus, I get these positions as reference calls and not as Ns (which I wanted, because they don't have support in my data).

Shouldn't all positions in the genome appear in the bcftools mpileup output and not only those where reads mapped? Is there a way I can generate vcfs will all the positions in the genome?

Thank you
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