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bioinformatics-centre / BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers
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Combine assertion error #28

Closed jjfarrell closed 4 years ago

jjfarrell commented 4 years ago

When running combine with scalpel calls and the prior vcf. I am getting this error. What type of vcf issue would trigger this?

bayesTyperTools: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.5_static/BayesTyper-1.5/src/bayesTyperTools/Combine.cpp:411: void Combine::combine(const std::vector<std::__cxx11::basic_string<char> >&, const string&, bool): Assertion contig_variants_it->second->alt(alt_allele_idx) != contig_variants_it->second->ref() failed.

jjfarrell commented 4 years ago

I figured it out. The normalization step had not yet been run for this vcf. After running the normalization step and getting rid of duplicates, the combine step worked fine.

bcftools norm -Oz -o scalpel.hg38.sites.norm.vcf.bgz -f /restricted/projectnb/casa/ref/GRCh38_full_analysis_set_plus_decoy_hla.fa -d all -cs scalpel.hg38.sites.vcf.gz