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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
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Error with same phase set, but different genotype ploides #233

Closed cnk113 closed 2 years ago

cnk113 commented 2 years ago 
In sample Adult_DSP_MG_multi_atac_cr, calls at
[2022-03-19 04:26:57] <EROR>     chr1:23392475-23392476 & chr1:23392475-23392479 were called in the
[2022-03-19 04:26:57] <EROR>     same phase set but have different genotype ploidies (3 & 2).

Version

octopus version 0.7.4 (develop c895357e)
Target: x86_64 Linux 5.8.0-50-generic
SIMD extension: AVX2
Compiler: GNU 9.3.0
Boost: 1_71

Command line to run octopus:

octopus -R /media/chang/HDD-1/reference_cellranger/refdata-cellranger-arc-GRCh38-mt-2020-A-2.0.0/fasta/genome.fa --config /home/chang/UMI.config -I possorted_bam.bam -o octopus.vcf --debug

I'm using UMI.config in your config directory.

octopus_debug.log.gz

dancooke commented 2 years ago

Closing as this is the same bug as described in https://github.com/luntergroup/octopus/issues/230. If you have a small test dataset that triggers the problem then that would be helpful - please add to the other issue.