Question: Error in vcf-subset while processing variants with multiple ALTs
gravatar for Molly
3.3 years ago by
Molly10 wrote:

Hello, I'm trying to obtain per-sample subsets from a vcf file using vcd-subset command of VCFtools. However, it doesn't work well. The error messages like:

The haplotype indexes in "0/2" do not match the ALT column .. 1:26608865 S0107

at /usr/local/share/perl/5.22.1/ line 172, <__ANONIO__> line 639. Vcf::throw(Vcf4_2=HASH(0x1fd8a98), "The haplotype indexes in \"0/2\" do not match the ALT column .."...) called at /usr/local/share/perl/5.22.1/ line 1941 VcfReader::parse_haplotype(Vcf4_2=HASH(0x1fd8a98), HASH(0x1eb1b20), "S0107") called at /usr/local/bin/vcf-subset line 162 main::vcf_subset(HASH(0x1a6e7b8)) called at /usr/local/bin/vcf-subset line 12

Checking the line 12 in the original vcf file, I found that REF column has A and ALT column has two candidate like G and T. So I think "0/2" means this locus of sample S0107 has heterozygous allele of A/T.

Due to this error, the subset file of S0107 doesn't contain "0/2" or "0/3" heterozygous variants with multiple ALT base, as well as above variant...this error occurred in all subset files. How can I solve this problem? Any possible suggestion is welcomed. Thank you in advance.

sequencing snp vcftools • 1.1k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 3.3 years ago by Molly10
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