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epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Apache License 2.0
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Paired mode analysis: control bam was deleted before it has been used #144

Closed kamyshova closed 3 years ago

kamyshova commented 4 years ago

Background

When a sample has a control sample is not NA, then Fonda runs paired mode analysis for this sample. Some of the tools (e.g Vardict) use the control bam for variant detection when they perform sample analysis. If the control sample script is executed before sample bam is required in the script of the "original" sample, the tool (e.g Vardict) will crash with the error that the control bam does not exist, because it has been deleted at the end of the control sample script.

Approach

I assume that it would be better to move the removal of all bams in the "original" sample script.

syansanofi commented 3 years ago

@kamyshova I agree this should be fixed, can you start this? Thank you