Question: Merge indel VCF files
0
gravatar for Randel
5.0 years ago by
Randel40
United States
Randel40 wrote:

I am merging tons of indel VCF files using vcf-merge. It does not work and I found these VCF files cannot pass the vcf-validation. Is there any way to merge indel VCF files? Thanks!

#CHROM    POS    ID    REF    ALT
1    62297    .    T    TCTTC
1    769138    rs59306077    CAT    C
1    772392    .    ACTTA    TCTTG

The error is

Could not determine the ploidy (nals=4, nvals=3). (TODO: ploidy bigger than 2)
15
 at /apps/software/vcftools/0.1.11/perl/Vcf.pm line 177
        Vcf::throw('Vcf4_0=HASH(0x28b56c0)', 'Could not determine the ploidy (nals=4, nvals=3). (TODO: ploi...', 15) called at /apps/software/vcftools/0.1.11/perl/Vcf.pm line 2408
        VcfReader::guess_ploidy('Vcf4_0=HASH(0x28b56c0)', 4, 3) called at /apps/software/vcftools/0.1.11/perl/Vcf.pm line 1764
        VcfReader::parse_AGtags('Vcf4_0=HASH(0x28b56c0)', 'HASH(0x2f8fc68)', 'HASH(0x27a50d8)', 'GA') called at /apps/software/vcftools/0.1.11/bin/vcf-merge line 453
        main::merge_vcf_files('HASH(0x27def48)') called at /apps/software/vcftools/0.1.11/bin/vcf-merge line 12
vcftools sequence merge indel vcf • 1.5k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Randel40
1

http://sourceforge.net/p/vcftools/mailman/vcftools-help/?viewmonth=201403&viewday=13

ADD REPLYlink modified 8 weeks ago by RamRS25k • written 5.0 years ago by marina.v.yurieva480

Thanks! I checked the link, but do you have specific suggestions?

ADD REPLYlink written 5.0 years ago by Randel40
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