% VCF2TSV(1) vcf2tsv | Convert VCF to TSV % Erik Garrison and other vcflib contributors
vcf2tsv - Converts stdin or given VCF file to tab-delimited format, using null string to replace empty values in the table.
vcf2tsv [-n null_string] [-g] [file]
vcf2tsv converts stdin or given VCF file to tab-delimited format, using null string to replace empty values in the table.
Specifying -g will output one line per sample with genotype information. When there is more than one alt allele there will be multiple rows, one for each allele and, the info will match the 'A' index
-h, --help
: shows help message and exits.
-g
: Output one line per sample with genotype information.
0 : Success
not 0 : Failure
>>> head("vcf2tsv -h",1)
usage: vcf2tsv [-n null_string] [-g] [vcf file]
vcf2tsv converts a VCF to a tabulated test file, e.g.
>>> head("vcf2tsv ../samples/sample.vcf")
#CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DB DP H2 NS
19 111 . A C 9.6 . . . . . . . . .
19 112 . A G 10 . . . . . . . . .
20 14370 rs6054257 G A 29 PASS . . 0.5 . . 14 . 3Use the -g switch to show genotypes
>>> head("vcf2tsv -g ../samples/sample.vcf")
#CHROM POS ID REF ALT QUAL FILTER AA AC AF AN DB DP H2 NS SAMPLE DP GQ GT HQ
19 111 . A C 9.6 . . . . . . . . . NA00001 . . 0|0 10,10
19 111 . A C 9.6 . . . . . . . . . NA00002 . . 0|0 10,10
19 111 . A C 9.6 . . . . . . . . . NA00003 . . 0/1 3,3The following commands run full regression tests:
run_stdout("vcf2tsv ../samples/sample.vcf", ext="tsv") output in vcf2tsv_4.tsv
run_stdout("vcf2tsv -g ../samples/sample.vcf", ext="tsv") output in vcf2tsv_5.tsv
Copyright 2020 (C) Erik Garrison and vcflib contributors. MIT licensed.