Error in bcf/vcf lifes

Question

[shakeelbiochemist]

I am facing problem in creating bcf and vcf files. When I try to make bcf file using samtools-1.2, it aborts by giving error
"Set max per-file depth to 8000"
However, when I do the same thing using older version of samtool-0.1.19, the bcf file is created.
Now, when calling variants using bcftools-1.2, it gives error "Failed to read bcf file."

However, When I used older version of bcftools-0.1.19, it makes vcf.gz file which is empty.

Kindly suggest is it samtools/bcftools version compatibility issue, or something else.

[Devon Ryan]

"Set max per-file depth to 8000" isn't an error message, it's just an informative statement that it's setting the maximum depth to 8000. We'd need to see the exact command you're issuing to be of any help.

[shakeelbiochemist]

Thank you Ryan for your response.

I used the command:

samtools mpileup -g -f /data/hg38.fa myfile.bam > myfile.bcf

samtools-1.2 aborts by giving the captioned statement "Set max depth....., and no output bcf formed....however using the samtools-0.1.19, a myfile.bcf file is generated.)

Then to call variants, when I used bcftools-1.2 command:

bcftools call -v -m -O z -o myfile.vcf.gz myfile.bcf

it aborted by giving the message could not read bcf file.

[Devon Ryan]

Well if myfile.bcf is empty then there's no point in running bcftools call. Try disabling BAQ, lowering the minimum base quality, and so on and see what happens. In general, you'll need to just have a look at the alignments in something like IGV and it should be somewhat apparent where the problem is (hopefully).