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quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.
MIT License
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added DANN scoring #41

Closed davemcg closed 6 years ago

davemcg commented 6 years ago

make script to pull DANN scoring and convert to vcf for vcfanno use

README cribbing from DANN abstract also included

brentp commented 6 years ago

did you test this? I would be surprised if this works because you're missing the ID, FILTER and QUAL fields in the "VCF".

davemcg commented 6 years ago

Uh, yes. I also didn't realize that vcfanno could match by ref / alt on non-vcf files. So you can actually just use the DANN file as is. 

dann_file="DANN_whole_genome_SNVs.tsv.bgz"
if [ ! -f $dann_file ]; then
    wget https://cbcl.ics.uci.edu/public_data/DANN/data/DANN_whole_genome_SNVs.tsv.bgz
    wget https://cbcl.ics.uci.edu/public_data/DANN/data/DANN_whole_genome_SNVs.tsv.bgz.tbi
fi

scoreset call for pathoscore.py --scores score-sets/GRCh37/DANN/DANN_whole_genome_SNVs.tsv.bgz:DANN:5:self

davemcg commented 6 years ago

Let me know if you want me to put another pull request in for the minimal make file. I can also provide a smaller DANN file for testing. It's rather slow to use, since like CADD, it is extremely dense.

brentp commented 6 years ago

A PR with the wget and the README would be great. thanks.