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Using PathSeqFilterSpark --ignore-alignment-contigs raises error #8766

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abdohlman opened this issue Apr 7, 2024 · 0 comments

abdohlman commented Apr 7, 2024

Bug Report

Affected tool(s) or class(es)

PathSeqPipelineSpark

Affected version(s)

GATK 4.2.2.0

Description

I called PathSeqPipelineSpark as follows:

I confirmed my bam file has a contig "chrEBV" in the bam header:

But unfortunately, for some reason PathSeq is not seeing it:
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Am I using the --ignore-alignment-contigs parameter incorrectly?

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