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FilterMutectCalls Error: 'IO exception while reading from contamination table'

mack812mack812 SpainMember
edited August 12 in Ask the GATK team


I am currently working on data from a tiny gene panel (~29 kb; target enrichment by amplicons) with deep coverage in most of the samples (mean coverage well above 1000x in most samples).

When running FilterMutectCalls I get the following error:

12:50:55.333 INFO  FilterMutectCalls - Shutting down engine
[August 12, 2019 12:50:55 PM GMT] done. Elapsed time: 0.05 minutes.

A USER ERROR has occurred: Encountered an IO exception while reading from M18-1500_IonCode_0103.contam.table.


This is how the contamination table looks like:

sample  contamination   error
M18-1500        0.002244490897093085    0.0034710127133886536

And this is how the segments.table looks like:

contig  start   end     minor_allele_fraction
chr4    55593464        55593464        0.46875059906546535

The command that I am running is (using GATK

gatk --java-options "-Xmx${mem_alloc_4k}" \
  FilterMutectCalls \
    -R $ref_fasta \
    -V $working_dir/output_files/${bam_basename}.unfiltered.vcf \
    --contamination-table ${bam_basename}.contam.table \
    --tumor-segmentation $working_dir/output_files/${bam_basename}.segments.table \
    -O $working_dir/output_files/${bam_basename}.filtered.vcf
Post edited by mack812 on

Best Answer


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