goVCFtoTable

goVCFtoTable is a tool for parsing a pVCF into a long "melted" tab-delimited format. I'm putting it together to process pVCF's created by GLnexus for use in a MariaDB database, so the tool is a very limited WIP.

Assumes that multiallelic sites are already split.

Prerequisites

goVCFtoTable uses the bgzf package from biogo for concurrent decompression.

$ go get github.com/biogo/biogo/hts/...

Usage

./goVCFtoTable input.vcf.gz output.tsv numThreads 

Comparison with bcftools for chromosome 21 from whole exome sequencing of >83000 people:

$ time bcftools query -f '[%CHROM:%POS:%REF:%ALT\t%SAMPLE\t%GT\t%GQ\t%AD\t%FT\n]' -i 'GT="alt"' chr21.vcf.gz > a.txt
real    75m6.131s                                                                                        │
user    74m44.026s                                                                                       │
sys     0m17.645s

$ time ./goVCFtoTable chr21.vcf.gz aaaaaaa.txt 1
real    21m14.092s                                                                                       │
user    27m25.216s                                                                                       │
sys     2m13.799s

$ time ./goVCFtoTable chr21.vcf.gz aaaaaaaaaa.txt 4 
real    14m45.272s                                                                                       │
user    37m10.282s                                                                                       │
sys     2m11.511s