I’m trying to build a reference table using a different reference genome. Variants were called with bcftools mpileup, bcftools call, and bcftools filter. I didn’t receive any errors on reading the ref from a fasta file (this is for the plant species Sorghum bicolor) nor did I receive any errors on …

This is awesome! First time Hail has been used for non-human analysis, I think :slight_smile:. I think the reference genome is fine, but there’s another problem… Your VCF has some weird patterns that don’t fall under the spec, which we don’t currently support. The VCF spec indicates that the indivi…

Tim: Thanks for your interest and suggestions. It was indeed awesome that I was able to bring the sorghum reference genome in to hail with little effort. I used bcftools to call the variants because I’m trying to replicate some previous results. For the purpose of working with hail, however, I’m go…

That will probably be easiest, though probably annoying to recall. Another thing – is Sorghum diploid, as it looks from the VCF line in the error message? Hail doesn’t currently support ploidy > 2, though we’ll add this at some point.

Good progress: I generated a new VCF using GATK’s haploTypeCaller and was able to import the resulting variants into a data matrix. There were a few multi-allelic loci which I had to eliminate before I was able to use the variant_qc method. From there I was able to complete all of the examples from…

Excellent! Let us know if you run into any other problems.

Just met the VCFParseError: ploidy > 2 not supported when we run hail 0.2.40 on a gatk4-mutect2 generated VCF. Wondering is there any time frame to support ploidy > 2 VCF since filtering out those multi-allelic variants does not seem to be reasonable in somatic calling scenario.

Your question is different than the earlier question in this thread, and it’s about Hail 0.2. Please make a new post for in the Help [0.2] category.

Matrix table error

Help [0.1]

obigbando August 6, 2020, 1:23am 9

Thanks for the suggestion; just did at VCFParseError: ploidy > 2

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Matrix table error

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