Entering edit mode
11.3 years ago
stolarek.ir
▴
700
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
