I have a several VCFs which are VCF which only contain information by chromosome. That is, there's a chromosome 1 VCF (with only chr1), a chromosome 2 VCF (with only chr2), etc.
I checked to make sure that these VCFs were valid via
$ vcf-validator chr1.vcf
which works---these are valid VCFs I was given.
Now, I would like to combine these VCFs into one VCF.
I naïvely tried the following
$ cat chr1.vcf chr2.vcf chr3.vcf ... chrX.vcf > total_chroms.vcf
This doesn't work properly though
$ vcf-validator total_chroms.vcf The header tag 'contig' not present for CHROM=chr1. (Not required but highly recommended.) Could not parse the line, wrong number of columns: [##fileformat=VCFv4.2\n] at /path/vcftools-0.1.14/perl/Vcf.pm line 172, <__ANONIO__> line 191016. Vcf::throw('Vcf4_2=HASH(0x1ae7208)', 'Could not parse the line, wrong number of columns: [##filefor...') called at /path/vcftools-0.1.14/perl/Vcf.pm line 335 Vcf::next_data_array('Vcf4_2=HASH(0x1ae7208)') called at /path/vcftools-0.1.14/perl/Vcf.pm line 3457 Vcf4_1::next_data_array('Vcf4_2=HASH(0x1ae7208)') called at /path/vcftools-0.1.14/perl/Vcf.pm line 2574 VcfReader::run_validation('Vcf4_2=HASH(0x1ae7208)') called at /path/vcftools-0.1.14//bin/vcf-validator line 60 main::do_validation('HASH(0x16ada68)') called at /path/vcftools-0.1.14//bin/vcf-validator line 14 $
What tools are available to merge these VCF's together into a total VCF?