Reorienting 1000 Genome VCF files, so that derived alleles are always ALT
Hello,
I am working with the 1000 Genomes Project phase 3 VCF files. I am trying to figure out how to reorient the REF and ALT alleles so that the derived allele is always the ALT.
I tried the --derived option in vcftools, but that apparently does nothing for the VCF output files.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Set ancestral alleles to upper case in vcf file
written by spiral01
-
Error while running R package rehh
written by shrutishreyajha •
-
subseting VCF by bcftools
written by miaowzai
-
Getting 1000 Genomes phase one MAF values
written by eurioste •
-
Changing to ancestral/derived states using vcftools
written by GabrielMontenegro
-
Finding only biallelic SNPs from the 1000GP BCF files
written by GabrielMontenegro
-
vcftools and multiple alternative allelles
written by oddmundn •
-
Recode VCF file according to ancestral alleles (AA)
written by abascalfederico
-
Ancestral allele in VCF files
written by thjnant
-
VCF file lacks alternative allele listing for most rs ids
written by devenvyas
