Integer overflow error

[bhanugandham]

Issue: Integer overflow error caused Mutect2 v4.1.4.0 to generate a stats file with a negative number. Solution is to change the int data type to long.

User report:

Hello, I've just adapted my pipeline to the new filtering strategies, while looking at the files I noticed that for a WGS run I obtained a stats file with a negative number:
[egrassi@occam biodiversa]>cat mutect/CRC1307LMO.vcf.gz.stats
statistic value
callable -1.538687311E9

Looking around about the meaning of the number I found https://gatkforums.broadinstitute.org/gatk/discussion/24496/regenerating-mutect2-stats-file, so I'm wondering if I should be worried by having a negative number of callable sites :/
What's more puzzling is that FilterMutectCalls after ran without any error.

Before running mutect I used the usual best practices pipeline, then:

gatk Mutect2 -tumor CRC1307LMO -R /archive/home/egrassi/bit/task/annotations/dataset/gnomad/GRCh38.d1.vd1.fa -I align/realigned_CRC1307LMO.bam -O mutect/CRC1307LMO.vcf.gz --germline-resource /archive/home/egrassi/bit/task/annotations/dataset/gnomad/af-only-gnomad.hg38.vcf.gz --f1r2-tar-gz mutect/CRC1307LMO_f1r2.tar.gz --independent-mates 2> mutect/CRC1307LMO.vcf.gz.log
    
gatk CalculateContamination -I mutect/CRC1307LMO.pileup.table -O mutect/CRC1307LMO.contamination.table --tumor-segmentation mutect/CRC1307LMO.tum.seg 2> mutect/CRC1307LMO.contamination.table.log

gatk LearnReadOrientationModel -I mutect/CRC1307LMO_f1r2.tar.gz -O mutect/CRC1307LMO_read-orientation-model.tar.gz 2> mutect/CRC1307LMO_read-orientation-model.tar.gz.log

gatk FilterMutectCalls -V mutect/CRC1307LMO.vcf.gz -O mutect/CRC1307LMO.filtered.vcf.gz -R /archive/home/egrassi/bit/task/annotations/dataset/gnomad/GRCh38.d1.vd1.fa --stats mutect/CRC1307LMO.vcf.gz.stats --contamination-table mutect/CRC1307LMO.contamination.table --tumor-segmentation=mutect/CRC1307LMO.tum.seg --filtering-stats mutect/CRC1307LMO_filtering_stats.tsv --ob-priors mutect/CRC1307LMO_read-orientation-model.tar.gz 2> mutect/CRC1307LMO_filtering_stats.tsv.log

This Issue was generated from your [forums]
[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/24633/mutect2-4-1-4-0-stats-file-with-a-negative-number/p1