stevekm / reportIT

IonTorrent variant reporting pipeline for clinical interpretation of cancer panel results
GNU General Public License v3.0
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split_df_col2cols function errors on too few columns #1

Closed stevekm closed 7 years ago

stevekm commented 7 years ago

In the script merge_vcf_annotations.py, function split_df_col2cols gives an error if the number of fields output by merge_df['AAChange'].str.split(':') is fewer than the number of replacement columns (5 given by default).

stevekm commented 7 years ago

In at least one case, a sample variant with no coding change somehow passed this step and generated a summary table, while the variant itself still lacked the Amino Acid change field in the annotation (e.g. p.R123H item). Need to investigate why the lack of this field results in errors for some cases but not others.

stevekm commented 7 years ago

This error also occurs if an intronic variant gets through filtering criteria and is processed by the function