vcfnulldotslashdot(1)

vcfnulldotslashdot converts single dots to ./. This is useful for some downstream analysis tools.

Section 1 libvcflib-tools bookworm source

Description

VCFNULLDOTSLASHDOT

NAME

vcfnulldotslashdot converts single dots to ./.

This is useful for some downstream analysis tools.

SYNOPSIS

vcf2tsv < file

DESCRIPTION

vcfnulldotslashdot converts single dots to ./.

This is useful for some downstream analysis tools.

EXIT VALUES

	0		Success
	not 0		Failure

EXAMPLES

vcf2tsv converts a VCF to VCF

>>> cat("../scripts/vcfnulldotslashdot data/issue_307_vcfnulldotslashdot.vcf")
##fileformat=VCFv4.1
##fileDate=20210209
##source=freeBayes v0.9.21
##reference=ahy.fa
##phasing=none
##filter="TYPE = snp & QUAL > 30 & AF > 0.05 & AF < 0.95 genotypes filtered with: GQ > 20"
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rab-field.AH13
contig71493_103113 50 . G A 79.0603 . AC=5;AF=0.078125;LEN=1;TYPE=snp GT ./.:0,0,0