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genepi / haplocheck

Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies
http://mitoverse.i-med.ac.at/
MIT License
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Issues with 1.0.8 output #10

Closed gevro closed 5 years ago

gevro commented 5 years ago

Hi, A few issues with the output of the new version.

1) The word "amount" is still used and is unclear what this means. 2) Major Heteroplasmy Level and Minor Heteroplasmy Level are now empty. This is probably a bug.

See example below: "Sample" "Contamination Status" "Overall Homoplasmies" "Overall Heteroplasmies" "Sample Coverage" "Major Haplogroup" "Major Haplogroup Quality" "Minor Haplogroup" "Minor Haplogroup Quality" "Amount Major Homoplasmies" "Amount Minor Homoplasmies" "Amount Major Heteroplasmies" "Amount Minor Heteroplasmies" "Major Heteroplasmy Level" "Minor Heteroplasmy Level" "Distance" "Clusters" "sample.bam" "NO" "33" "25" "3382" "U8b1b2" "0.926" "U8b1b2" "0.911" "26" "26" "0" "0" " " " " "0" ""

seppinho commented 5 years ago

Thanks. I updated the code to match the documentation: "Major Homoplasmies Count" and so on.