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Inquiry about "run_charger.sh" #1

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paulhtyang opened this issue Jun 4, 2018 · 0 comments
Open

Inquiry about "run_charger.sh" #1

paulhtyang opened this issue Jun 4, 2018 · 0 comments

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@paulhtyang
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Hi Kuan,

I'm trying to follow the protocols of script coded in "run_charger.sh" on our data sets. There are data sources (cross-reference) has to be included, e.g.
mmGenes="/gscmnt/gc2737/ding/Analysis/Germline/CharGer/20160301_Rahman_KJ_KH_gene_table_CharGer.txt"
mmVariants="/gscmnt/gc2737/ding/Analysis/VariantLists/emptyRemoved_20160428_pathogenic_variants_HGVSg_VEP.vcf"
hotspot="/gscmnt/gc2737/ding/Analysis/Germline/CharGer/MC3.noHypers.mericUnspecified.d10.r20.v114.clusters"

Could you please show me the more detail way how to obtain these cross-references further more? Thank you very much.

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