VCFtools Ploidy Issue

[ercfrtz]

I am using vcftools to merge 2 files, 1 from GATK and 1 from Platypus to do some comparisons, but when I do, I get the following error:

Could not determine the ploidy (nals=4, nvals=3). (TODO: ploidy bigger than 2)
15
 at /home/eric.fritz/vcftools_0.1.11/perl//Vcf.pm line 177
        Vcf::throw('Vcf4_0=HASH(0x1e55208)', 'Could not determine the ploidy (nals=4, nvals=3). (TODO: ploi...', 15) called at /home/eric.fritz/vcftools_0.1.11/perl//Vcf.pm line 2408
        VcfReader::guess_ploidy('Vcf4_0=HASH(0x1e55208)', 4, 3) called at /home/eric.fritz/vcftools_0.1.11/perl//Vcf.pm line 1764
        VcfReader::parse_AGtags('Vcf4_0=HASH(0x1e55208)', 'HASH(0x1e77a68)') called at /home/eric.fritz/vcftools_0.1.11/perl/vcf-merge line 461
        main::merge_vcf_files('HASH(0x1e3a4a8)') called at /home/eric.fritz/vcftools_0.1.11/perl/vcf-merge line 12

Is there a way to get around this or fix it? Thanks.

[menglin44]

try -R?

Hi ercfrtz,

have you tried $vcf-merge -R 1.vcf.gz 2.vcf.gz ... ?