ding-lab / pancanatlasgermline Goto Github PK

HI. I wonder if you could tell me how to access the clinical data of the 10389 pancan germline cases.

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.

作者你好，你们发在cell上的这篇文章“Pathogenic Germline Variants in 10,389 Adult Cancers”非常棒。看完之后由于找不到您的邮箱地址，所以只能在这请教一下：在具体进行多个软件结果合并的时候，多个软件是如何做到多参数的统一的？是以默认参数在多个软件跑出结果后进行合并时按照筛选条件进行筛选，还是先在软件里设定好筛选条件跑出结果后再进行合并？