From 63a0a0a876eaf8d575c54ca93d32ec76e2522a84 Mon Sep 17 00:00:00 2001 From: Zoe Anne Dyson Date: Sat, 13 Nov 2021 13:04:36 +0000 Subject: [PATCH] Update README.md --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c548fec..7fd1949 100644 --- a/README.md +++ b/README.md @@ -37,9 +37,9 @@ File PASS LowQual Percent_LowQual Non-exclu ![image](https://user-images.githubusercontent.com/8507671/141644457-7f01fa9c-bc63-4ea9-b455-7f0cac2391a8.png) -## Key information +## Example usage and key information -### Cluster modules to load (and command to load them) before running script: +### Cluster modules (and dependancies) to load before running the script: ``` module load bsub.py/0.42.1 @@ -48,6 +48,8 @@ module load bcftools/1.2--h02bfda8_4 module load samtools/0.1.19--h94a8ba4_6 ``` +- Note bsub.py is only required if submitting batches of jobs to the Sanger lsf cluster system. + ### Example usage (running from command prompt): ``` @@ -59,7 +61,7 @@ python2 GHRU_SNV_Stats_Generator.py --bcf *.bcf --excluded_regions CT18_repeats_ bash run_bcf_batches.sh Wong2015_Tanzania ``` -#### Notes for selecting subsets to analyse: +#### Suggestions for selecting subsets of a larger dataset to analyse ``` while read file; do ln -s /lustre/scratch118/infgen/team216/jk27/typhinet/*/ghru_mapping/filtered_bcfs/${file}.filtered.bcf ./; done