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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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web server and package #39

Closed anna-panchenko closed 4 years ago

anna-panchenko commented 4 years ago

the webserver and package produce different results:

(env_mutagene) Annas-MBP:mutagene panch$ mutagene signature -i TSVC_variants_IonXpress019(BCMDS-116).vcf -g hg38 -f VCF -s 10 -U sample signature exposure mutations VCF 2 0.0535 3 VCF 3 0.1164 7 VCF 4 0.1134 7 VCF 5 0.1244 7 VCF 6 0.3912 23 VCF 7 0.1603 9 VCF 8 0.0109 1 VCF 9 0.0274 2 (env_mutagene) Annas-MBP:mutagene panch$ mutagene signature -i TSVC_variants_IonXpress019(BCMDS-116).vcf -g hg38 -f VCF -s 10 sample signature exposure mutations VCF 1 0.0144 1 VCF 3 0.1123 7 VCF 4 0.0514 3 VCF 5 0.1074 6 VCF 6 0.1604 9 VCF 7 0.0341 2 VCF 9 0.0328 2

neksa commented 4 years ago

Investigated. The reason is different input signatures - they differ in rounding/mantissa. Also need to specify -m compat for reproducibility.