vcf2msa

Conversion of a multi-sample VCF file to a multiple sequence alignment in FASTA format using htslib

Compilation:

make

Usage

./vcf2msa <reference fasta> <vcf>

output: within the current directory, saves a fasta file per sample contained in the VCF file.

ie. if the VCF file contains samples S1, S2, and S2, S1.fa, S2.fa and S3.fa will be produced. The concatenation of these fasta files is the multiple sequence alignment.

TODO:

• check name of input sequence against the sequence name associated with each VCF record
• output the reference sequence as part of the MSA
• check that the input VCF is sorted
• output one fasta file instead of multiple fasta files?
• support nested variants
• support subsetting of samples (currently does the MSA for ALL samples)
• support or ignore complex variants, ie. <CNV>, <DUP>, etc.