v0.2.0

VCF2tFasta Version 0.2 prior to 2024 updates

Convert gVCF files to transposed fasta format (tfasta, indexed and compressed).

Jordi Leno-Colorado

Usage:

./gVCF2tFasta -v input.vcf(.gz) -r reference.fa(.gz) -o outputname -n chromosomes.txt

Note: Structural Variants are considered as missing data (N)

Flag Options:

-h        Help and exit
-v        Input VCF file
-r        Reference Fasta file
-o        Output compressed tFasta filename (without extension)
-n        File with chromosome(s) to convert and its length
-i        Imputation (Only use with VCF files, not gVCF files):
            0 if missing data in VCF is equal to N in tFasta
            1 if missing data in VCF is equal to reference fasta in tFasta
            Default value is 0

To compile:

make -f nbproject/Makefile-Release.mk build/Release/GNU-Linux/main.o
mkdir -p build/Release/GNU-Linux
rm -f "build/Release/GNU-Linux/main.o.d"
g++ -std=c++0x -lz   -c -O2 -MMD -MP -MF "build/Release/GNU-Linux/main.o.d" -o build/Release/GNU-Linux/main.o sources/main.cpp
/usr/bin/make -f Makefile CONF=Release

Examples:

Convert a compressed single individual VCF file to a compressed tFasta file

../bin/gVCF2tFasta -v example.vcf.gz -r ref.fa.gz -o example -n ref.fa.fai

Convert a VCF file with the SNPs of a pool to a compressed tFasta file

../bin/gVCF2tFasta -v pool_p10.vcf -r ref.fa.gz -o pool -n ref.fa.fai

Convert a compressed multiple individual VCF file to a compressed tFasta file

../bin/gVCF2tFasta -v ./gatk_combined.vcf_10lines.recode.vcf.gz -r ./pdulcis26.contigs_Pd1-8.fa -o ./TEST_almond_10lines -i 0 -n ./pdulcis26.chromosomes.lengths