missing REF and ALT in vcf
1
0
Entering edit mode
2.3 years ago
raalsuwaidi ▴ 100

is there a tool or a way where i can select some SNPs and have the values for the REF and ALT set to missing (replaced by ".") or do i have to do pure coding?

REF SNP VCF ALT • 852 views
ADD COMMENT
1
Entering edit mode
2.3 years ago
bcftools view --uncalled in.vcf
bcftools view -i 'COUNT(GT="mis")>0'  in.vcf
ADD COMMENT
0
Entering edit mode

Thank you for such a fast response.

But I actually want to change the genotype values to be missing so I can run it through imputation. Will you be able to help?

ADD REPLY

Login before adding your answer.

Traffic: 1013 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