Fixing bug in FilterMutectCalls for GVCFs #8458
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ahaessly
approved these changes
Aug 8, 2023
| // set tumorAD to 0 for symbolic alleles so it won't contribute to overall AD | ||
| symIndexes.forEach(i -> tumorADs[i] = 0); | ||
| // set tumorAD to 0 for symbolic alleles so it won't contribute to overall AD, ADs include reference allele so add one to the index | ||
| symIndexes.forEach(i -> tumorADs[i+1] = 0); |
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I just want to make sure that this can't try to read past the end of the array. I think that the non-ref allele is always at the end and as long as that is not a symbolic allele, I think you should be ok. Just want to make sure that's correct.
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It should be correct, but would it be better to put an Assert in for the lengths of the Arrays?
rickymagner
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Nov 28, 2023
* fixing bug in FilterMutectCalls for GVCFs * adding assert
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When using GVCFs with Mutect2 (for example with the Mitochondria mode), in the filtering step ADs for symbolic alleles are set to 0 so it doesn't contribute to overall AD. There was an off-by-one error that removed the alt allele AD rather than the <NON_REF> allele AD. This led to
NaNs and errors when a site had no ref reads (for example a GT of [ref,alt,<NON_REF>] and AD of [0,300,0] would accidentally be changed to an AD of [0,0,0] if the alt index was removed instead of the <NON_REF> index).The test changes the AD in one of the sites of the NA12878.MT.g.vcf to have 0 ref reads which fails without the fix in
SomaticClusteringModel.This addresses #8455.