Question: Samtools Bcf To Vcf Problem
gravatar for Anjali
7.5 years ago by
Anjali60 wrote:

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 | 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 • 7.4k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Anjali60

are you sure that the bcf file is not empty?

ADD REPLYlink written 7.5 years ago by Giovanni M Dall'Olio26k

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).

ADD REPLYlink written 7.5 years ago by madkitty590
gravatar for madkitty
7.5 years ago by
madkitty590 wrote:

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

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by madkitty590
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