Hi.

I have a problem with my variant calling using samtools. I'm interested in vcf file with indels in my bam file.

I run the following command:

 samtools mpileup -Ruf genome.fa merged.bam | bcftools view -gc - > merged.vcf

This gives:

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

The output is only chrM and run ends with:

[bcf_sync] incorrect number of fields (6 != 5) at 0:11894

When I try hacking this and deleting chrM:

samtools mpileup -Ruf genome.fa merged.bam | grep -v "chrM"| bcftools view -gc - > merged.vcf

out info:

[afs] 0:0.000

The output contains only metadata (lines starting with #)

Does anyone know the solution for this?

I really want to avoid pileup parsing, since this is really a pain.

EDIT: Problem solved. Used mpileup -Buf