{"push_id":951169545,"size":7,"distinct_size":3,"ref":"refs/heads/facets_ann","head":"e9574b0af3220a4c2b38ca822f01e8805ff87e74","before":"a8dfdee4aa78847993c989673fe218e519dc046a","commits":[{"sha":"8a703978aa51d037518455c5b588e167fe15368f","author":{"email":"f7dc43fb05ba7df7e769446605d0d8a8ab1011c4@ino.pm","name":"Ino de Bruijn"},"message":"Add facets/absolute/custom to excel and plot\n\n- Get cancer_cell_frac Pr_somatic_clonal and ccf_CI95_low from absolute results.\n- Get facets LOH from facets/geneCN.em.reviewed.txt. Basically the original\n  facets file after reviewing\n- Get whatever other type of annotations for the mutations from\n  summary/annotation.tsv merge on TUMOR_SAMPLE CHROM POS REF ALT columns\n- Add MUTATION_SUMMARY sheet in excel that lists all NS and S mutations. Remove\n  annotations that are not NS and S from | separated columns\n- Add likely_pathogenic\n        - for snv: fathmm_pred is \"CANCER\" and chasm score > 0.3\n        - for indel: dbNSFP_PROVEAN_PRED is D or dbNSFP_MutationTaster_pred is\n          D\n- Add cancer_gene\n        - either cancer_gene_census, kandoth or lawrence is true\n- Plot heatmaps for NS mutations in all samples using the excel file\n        - ccf from absolute\n        - LOH from facets\n        - likely_pathogenic\n        - cancer_gene","distinct":false,"url":"https://api.github.com/repos/jrflab/modules/commits/8a703978aa51d037518455c5b588e167fe15368f"},{"sha":"9219dd1cbe7c8cd72f896e0cbb119fe5572c45db","author":{"email":"f7dc43fb05ba7df7e769446605d0d8a8ab1011c4@ino.pm","name":"Ino de Bruijn"},"message":"Mutation summary add optional ExAC_AF threshold\n\nIn case of a bad sample, it can be useful to set a threshold on the ExAC_AF\ncolumn. This adds a config variable EXCEL_MAX_EXAC_AF to set the max value for\nmutations in the mutation_summary excel sheet, it is 1 by default.","distinct":false,"url":"https://api.github.com/repos/jrflab/modules/commits/9219dd1cbe7c8cd72f896e0cbb119fe5572c45db"},{"sha":"6804e4c77962b03942c35864400efb28cabae1ee","author":{"email":"f7dc43fb05ba7df7e769446605d0d8a8ab1011c4@ino.pm","name":"Ino de Bruijn"},"message":"Fix CHASM prediction inversion","distinct":false,"url":"https://api.github.com/repos/jrflab/modules/commits/6804e4c77962b03942c35864400efb28cabae1ee"},{"sha":"f4ad9e500af397edbc28dbad02acfbb9de29c392","author":{"email":"272352ae9315b9d92387b3927dc543431e64fb05@mm.st","name":"Raymond Lim"},"message":"Merge pull request #91 from inodb/merge_multisource_to_summary\n\nAdd facets/absolute/custom to excel and plot","distinct":false,"url":"https://api.github.com/repos/jrflab/modules/commits/f4ad9e500af397edbc28dbad02acfbb9de29c392"},{"sha":"477a2b92ba045241eb782bd0793f1fb3a672bb85","author":{"email":"272352ae9315b9d92387b3927dc543431e64fb05@mm.st","name":"raylim"},"message":"default to not annotate facets to vcf files","distinct":true,"url":"https://api.github.com/repos/jrflab/modules/commits/477a2b92ba045241eb782bd0793f1fb3a672bb85"},{"sha":"3b59f5b04c999e76bbb901bb2fd0108cec83b8d4","author":{"email":"272352ae9315b9d92387b3927dc543431e64fb05@mm.st","name":"raylim"},"message":"Merge branch 'master' of https://github.com/raylim/modules into facets_ann","distinct":true,"url":"https://api.github.com/repos/jrflab/modules/commits/3b59f5b04c999e76bbb901bb2fd0108cec83b8d4"},{"sha":"e9574b0af3220a4c2b38ca822f01e8805ff87e74","author":{"email":"272352ae9315b9d92387b3927dc543431e64fb05@mm.st","name":"raylim"},"message":"mutation pathogenicity for missense and fs/ss/truncating","distinct":true,"url":"https://api.github.com/repos/jrflab/modules/commits/e9574b0af3220a4c2b38ca822f01e8805ff87e74"}]}