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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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Frameshift simulation bug #1

Closed ctokheim closed 7 years ago

ctokheim commented 8 years ago

Gene name was NAN, and missing strand information caused other columns to be out of order. Ultimately resulting in changing of column dtypes that causes an error in the code. The simulated MAF file produced the following line:

       Gene     strand   Chromosome    Start_Position End_Position  \
597232  NaN  143080161  143080176.0  NNNNNNNNNNNNNNNN            -

       Reference_Allele    Tumor_Allele Context       DNA_Change  \
597232                -  c.768_784.0del     p.?  Frame_Shift_Del

       Protein_Change Variant_Classification
597232            NaN                    NaN
ctokheim commented 7 years ago

Just drop these mutations. Usually happens very sporadically to one simulated indel.