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 ?