Question: Best way to fill VCF with ancestral allele info AA for each SNP hg19
gravatar for tcgp
3.0 years ago by
tcgp0 wrote:

Hi all,

I am currently working with some full-genome human sequence data (mapped to hg19) and created VCF (called only SNPS) files from my BAM files with gatk. For each SNP in my VCF I need the information about the ancestral allele (AA in VCF INFO field). I was wondering: what is the best way to add this information to my VCFs? I was reading about gatk annotator and oncotator and later found vcftools fill-aa, which can take a fasta file of ancestral alleles for each position as input to add this to the VCF.

However, on the 1000Genomes website I could only find the ancestral allele alignments from the pilot phase and not for phase3. There must be a better way than obtaining the ancestral state for each position from the 1000Genomes phase3 VCFs...

So which tool coupled with which data-source allows me to add this information to my VCFs ?


hg19 gatk vcf ancestral allele • 1.5k views
ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 3.0 years ago by tcgp0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1928 users visited in the last hour