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extend readme
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sophie22 committed May 7, 2022
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Expand Up @@ -13,3 +13,11 @@ Generate a report that lists any genes that have less than 100% coverage at 30x.

- Ideally using python, write a script that takes the sambamba output and generates a report listing any genes that have less than 100% coverage at 30x
- This script should be able to be applied to any gene panel

## Version 0.0.1
sambamba output file was converted to a tsv by replacing whitespaces with tabs by the following command:
`sed -e 's/ /\t/g' NGS148_34_139558_CB_CMCMD_S33_R1_001.sambamba_output.txt > NGS148_34_139558_CB_CMCMD_S33_R1_001.sambamba_output.tsv`
A Python script was written in a new virtual environment (using Python 3.8.0 and packages as listed in the `requirements.txt`) to identify genes that have at least one exon with suboptimal coverage, and write the gene symbols into an output file.

## Version 0.0.2
Calculate a combined percentage coverage value for the whole gene and identify genes with less than 100% coverage at 30x. Write information about each gene with suboptimal coverage to an output file.

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