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Samtools Bcf To Vcf Problem

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

vcf
• 10,498 views • link
updated by Biostar Biostar • written by Anjali • Anjali

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).

• 1 views • link
written by madkitty madkitty

1 answer

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

• 0 views • link
written by madkitty madkitty

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