I have vcf files that I wish to combine so that any variants with matching positions are combined also. For example, if I have a variant in one file at position 123 and also one in another file there, I want that information to be combined in the genotype info.
The actual variants will be the same (T->G in one file will always be T->G in the other) as they have been created using the same reference data.
Is this possible to do in one go with any tool?
Thanks for your reply. Yes each file is a single individual. I am trying to combine the vindija and altai neanderthal vcf data. Both have been created using the hg19 as reference and I just want to combine the two vcf files in one.
I think that should do the trick for you then. Let me know if you have any issues.
GATK asks for a reference genome in fasta format. In this case I need the hg19 reference (obtained here: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/). Is the chromFa.tar.gz the correct reference file for the hg19 build?
You'll want to download the hg19.2bit file and then use their utility to convert it to a Fasta file.