vcf2fasta creates sequences for each sample in a VCF file.
I have written this script to help me with a phylome analysis.
It requires:
* a genome reference fasta file
* a VCF file.
* a BED file with the regions to process
It will substitute the alleles found in the VCF file into the genome reference to create the sample sequences.
It will create a fasta file for each region found in the BED file. In each fasta file the aligned sequence for each sample in the VCF file will be written.
A file with the coverages found in a list of BAM files can be optionally given. This file can be generated with the command:
$ samtools depth -f bam_list.txt -q 20 -Q 55 | gzip > coverages.csv.gz
If this coverage file is given all the positions with a coverage lower than a given threshold will be set to N.
Other alternatives to this script are: GATK's FastaAlternateReferenceMaker and bcftools consensus.