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ikalatskaya / ISOWN

Apache License 2.0
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External database URLs are out of date. #32

Open BiodeB opened 6 months ago

BiodeB commented 6 months ago

Hi,

I want to start by saying thank you for creating such wonderful software. But when I was following this https://github.com/ikalatskaya/ISOWN, I noticed that several of the URLs listed in the ISOWN manual were no longer active when I was downloading the EXTERNAL DATABASES.

I've downloaded the data from a few of the sites that are, COSMIC: COSMIC v96, CosmicCodingMuts.vcf.gz and CosmicNonCodingVariants.vcf.gz files downloaded from https://github.com/Illumina/NirvanaDocumentation/blob/master/docs/data-sources/cosmic.mdx

dbSNP: https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/00-All.vcf.gz

ExAC: https://storage.googleapis.com/gcp-public-data--gnomad/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz

However, I'm unable to find the latest location of PolyPhen WHESS and the mutation assessor; they are not present at the specified place. 

wget ftp://genetics.bwh.harvard.edu/pph2/whess/polyphen-2.2.2-whess-2011_12.tab.tar.bz2 --no-passive-ftp
wget http://mutationassessor.org/r2/MA.scores.hg19.tar.bz2 --no-passive-ftp

It will be great help if someone please update the location of those databases. Thanks