Hi everyone. I'd like to create a new fasta file containing all sequences for which I called variants in a vcf file. I can only get one sequence, but I would like to rebuild the sequence for all my samples. I know I can do it individually, but is there any tool to do it for all my samples at once? Thank you very much!
How about a simple iteration of vcf-consensus -s <sample_name> . The new version also gives an option to use IUPAC ambiguity codes for hetrozygotes or no-calls.
See this post. It may be at least partially helpful.
vcf to MAF to fasta