Question: Error in vcf-subset while processing variants with multiple ALTs
gravatar for Molly
2.3 years ago by
Molly0 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 • 780 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by Molly0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1623 users visited in the last hour