Question: Best way to fill VCF with ancestral allele info AA for each SNP hg19
gravatar for tcgp
4.6 years ago by
tcgp20 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 • 2.2k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 4.6 years ago by tcgp20
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