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szsctt / intvi_other-tools

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vifi input files #3

Open TheBready opened 3 years ago

TheBready commented 3 years ago

@szsctt I have some issues getting all the input files for vifi and the HG37:

mappability: "../vifi-test/data_repo/GRCh38/hg38full_k35_noMM.mappability.bedgraph" mappability_exclude: "../data/references/GRCh38/ENCFF356LFX.bed" genes: "../data/references/GRCh38/hg38.gencode.v35.annotation.genes.gff3" exons: "../data/references/GRCh38/hg38.gencode.v35.annotation.exons.gff3" oncogenes: "../data/references/GRCh38/hg38.gencode.v35.annotation.genes.gff3" centromeres: "../data/references/GRCh38/centromeres.bed" conserved_regions: "../data/references/GRCh38/exclude.cnvnator_100bp.GRCh38.20170403.bed" segdup: "../data/references/GRCh38/genomicSuperDups.bed"

Did you already use the HG37 for this?

szsctt commented 3 years ago

I will add some documentation today to make usage of the various tools a little easier :)

It's a bit frustrating that ViFi doesn't say that it requires these files, but I tried running it without and I couldn't get it to work. You can find more information about ViFi on its github page, and there they link to the required files for hg19/GRCh37. The files for GRCh38 are at the Amplicon Architect page.