BCFtools variant calling format

Question

[amy16]

I run the command line below (as a job script on HPC):

samtools mpileup -uf Ca_v1.0_kabuli_ref.fasta B1_C.bam
bcftools view -bvcg B1_C.raw.bcf

I find the output file is generated in the slurm-out (the HPC specific job run output file). I am not sure if I am going wrong with the script somewhere.

Answer 1

[Ram]

That's because you're not redirecting the output of the bcftools command, so it writes to STDOUT, which HPC systems dump to the file in their -o or -oo parameter. Add a >out.vcf to your bcftools command and everything will be fine.

[amy16]

bcftools view -bvcg B1_C.raw.bcf >B1_C.vcf I tried it.. it is still not generating a separate output file

[Ram]

The command is incomplete - -c needs an INT to work off of, and I'm not sure if -g and -v have defaults. Also, what is -b? What version of bcftools are you using?

It would also help if you looked at the STDERR file from the job.