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KarchinLab / probabilistic2020

Simulates somatic mutations, and calls statistically significant oncogenes and tumor suppressor genes based on a randomization-based test
http://probabilistic2020.readthedocs.org
Apache License 2.0
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summary output dropping genes with only indels #4

Open ctokheim opened 7 years ago

ctokheim commented 7 years ago

It appears the summary output is not saving genes that only have indel mutations.

Gene       Tumor_Sample    Tumor_Type      Chromosome      Start_Position  End_Position    Variant_Classification  Reference_Allele        Tumor_Allele    Protein_Change  DNA_Change
A1CF    ICGC_0063       Pancreatic Adenocarcinoma       10      52573738        52573738        Missense_Mutation       C       T       p.R401Q c.?
ABCB4   TCGA-IB-7897    Pancreatic Adenocarcinoma       7       87074281        87074282        Frame_Shift_Indel       -       T       p.S339fs        c.?