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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Minigraph-cactus result to PanGenie input variant vcf #1034

Closed ld9866 closed 1 year ago

ld9866 commented 1 year ago

Dear developer: I noticed that PanGenie was used for genotyping analysis in the article. However, when we input the vcf file, an error message was displayed. May I ask how you convert the format of the vcf file from Minigraph-cactus as the input file for PanGenie? Code: PanGenie -i test.fq -r reference.fa -v variant.vcf -t 10 -j 10 Result: VariantReader: skip variant at 1:1 since alleles contain undefined nucleotides: terminate called after throwing an instance of 'std::runtime_error' what(): VariantReader::VariantReader: Found invalid genotype. Genotypes must be diploid (.|. if missing).

glennhickey commented 1 year ago

You cannot feed the output of minigraph-cactus directly into pangenie: some processing on the vcf is required first. Details on how to reproduce our experiments can be found here: https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/mc-paper/hprc/README.md#sv-genotyping-with-pangenie

Also feel free to contact PanGenie's author directly here: https://github.com/eblerjana/pangenie

ld9866 commented 1 year ago

Thanks for your reply! We will try in time. Best day!