Samtools Bcf To Vcf Problem

Question

[Anjali]

Hi I have a bcf file generated using bcftools(samtools), which I further wanted to convert to vcf format. I used the following command:

bcftools view ../bcf/test.bcf | vcfutils.pl varFilter -D 8000 > test.vcf

The corresponding vcf file only generated the header and not the body.

I have used this command 2 months before on a different dataset and it worked well. I have the same Human fasta index file as a refernce. I can not figure out what is the problem now.

Can anyone help me??

I look forward to your reply

[Giovanni M Dall'Olio]

are you sure that the bcf file is not empty?

[madkitty]

you should also visualize your bcf file with your own eyes, open it with 'view' and check the data until the very end (unless it's too big).

Answer 1

[madkitty]

try to grab the header first (with grep or anything you like) write in a file with the same name as your output file and then overwrite to your output file (with the same command you have here)

.. not sure that would work but I would give it a try