VCF filtering by depth

Question

[perezalquicira]

Hi, I am trying to filtering a vcf file by --minDP however the log file indicates that it is not filtering out any SNP, any clue about this problem? I tried different values for DP but is not working any of them (I do have DP information in my vcf file)

/data/storage/software/vcftools/bin/vcftools --vcf /home/jperez/croc/res_cornell/vcf_croc_addinCONTIG.vcf --recode-INFO-all --minDP 100 —-out minDP_100.vcf

Thanks

[mike229lin]

you should try --min-meanDP instead of --minDP if you didn't solve that problem. I'm also wondering why vcftools write some argument making user a little bit confusing.

Like --min-meanDP & --minDP or --minQ and --minGQ

Answer 1

[agata88]

I have a script that can do what you need. 

#! python

import sys
import os
import vcf

vcf_reader = vcf.Reader(open("file.vcf", 'r'))
vcf_writer = vcf.Writer(open('out.vcf', 'w'), vcf_reader)
for record in vcf_reader:
    if record.INFO['DP']>100:
        vcf_writer.write_record(record)

Hope it helps,
Best,
Agata

[ja4123]

How to filter AF in vcf file with that way? There is a KeyError.

Answer 2

[igor]

VCFtools allows filtering. See the "--minDP" argument.

https://vcftools.github.io/man_latest.html

Answer 3

[perezalquicira]

Thanks Agata, I have mac and try to run the script and I got this message:

Traceback (most recent call last): File "DP.py", line 3, in <module> import vcf ImportError: No module named vcf

[agata88]

You need to install PyVCF module for example from here https://pypi.python.org/pypi/PyVCF Make sure that it is compatible with your python version! Best, Agata