How can I convert heterozygous genotype data to missing data?
1
0
Entering edit mode
2.7 years ago

I want to remove heterozygous genotype data in multi-samples VCF. At first I used bcftools filter -e option, but it made output VCF that lots of sites are deleted because of few heterozygous genotypes. I think this result is not suitable to search valid SNPs. Therefore, I want to convert heterozygous genotype data to missing data for filteration using vcftools later. Could you recommend effective tools?

vcf convert heterozygous missing • 1.7k views
ADD COMMENT
0
Entering edit mode

You have not explained very well what you want to do. Can you show the commands that you have already used, and state what is the purpose (in your mind) of each command?

ADD REPLY
1
Entering edit mode
2.7 years ago

You can do this using the bcftools plugin setGT:

$ bcftools +setGT input.vcf -- -t q -i 'GT="het"' -n "./." > output.vcf

But Kevin's questions persists: Why do you think this is useful?

fin swimmer

ADD COMMENT

Login before adding your answer.

Traffic: 2383 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6