Skip to content

Commit

Permalink
add v0.0.2 description
Browse files Browse the repository at this point in the history
  • Loading branch information
sophie22 committed May 7, 2022
1 parent 0a322af commit 928c60b
Showing 1 changed file with 7 additions and 3 deletions.
10 changes: 7 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,18 @@ 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
## What is required to run this script?
### What is required to run this script?
A new virtual environment was created using Python 3.8.0 and packages installed from the `requirements.txt`.
The 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`

## What does this script do?
## Version 0.0.1
### What does this script do?
Using the `percentage30` column, regions with less than 100% coverage at 30x are identified and a list of unique gene symbols is saved to an output file.

Command used to generate the example output: `python genes_coverage.py NGS148_34_139558_CB_CMCMD_S33_R1_001.sambamba_output.tsv`

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

0 comments on commit 928c60b

Please sign in to comment.