Entering edit mode
2.3 years ago
taniamahmood38
▴
60
Dear all,
I have a VCF file from which I want to compute site frequency spectrum (sfs) statistics using rehh package on R. There I came to know that rehh accepts polarized vcf file meaning the file which has ancestral allele information in it (the AA tag), but my vcf doesn't has this info. Kindly tell me the tool and command to add the AA tag in vcf file. Any help would be highly appreciated
Thanks in advance
Thanks for the help. But kindly clarify that if the vcfancestralallele command will work on any specie vcf file other than human?
Thanks
no, unless you have file similar to http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/
Okay but I dont have this file so is there any other way to do that? Kindly let me know, thank you