I have been trying to generate FASTA sequences for a region using a multi-sample VCF file and a reference genome. I have 70 diploid individuals in the VCF in total, and what I finally want is to obtain 140 sequences, two for each sample. Output format like multiple sequence alignment is also great for me. Is there any script/tools can do this?
I have tried FastaAlternateReferenceMaker (from GATK) but it only gives me a consensus sequence for all the samples.
Any help will be greatly appreciated!