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zadyson authored Nov 13, 2021
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## What is in this repo?
**GHRU_SNV_Stats_Generator.py** - python script for extracting high (PASS) and low (LowQual) SNV calls from bcf files produced by the GHRU mapping pipeline.
**CT18_repeats_phages_excluded_regions.tsv** - Phage and repeat regions normally excluded from phylogenetic analysis of S. Typhi (CT18: accession no. AL513382).
**run_ghru_snv_stats_in_batches.sh** - wrapper script for batch submission of jobs via lsf cluster system.
**Plot_Low_Qual_SNV_Distribution.R** - example R plotting script - visualises the distribution of low qual SNV calls throughout the reference sequence both before an after the removal of those falling within repetitive and phage regions (normally excluded for phylogenetic analysis).
**GHRU_SNV_Stats_Generator.py** - python script for extracting high (PASS) and low (LowQual) SNV calls from bcf files produced by the GHRU mapping pipeline.\

**CT18_repeats_phages_excluded_regions.tsv** - Phage and repeat regions normally excluded from phylogenetic analysis of S. Typhi (CT18: accession no. AL513382).\

**run_ghru_snv_stats_in_batches.sh** - wrapper script for batch submission of jobs via lsf cluster system.\

**Plot_Low_Qual_SNV_Distribution.R** - example R plotting script - visualises the distribution of low qual SNV calls throughout the reference sequence both before an after the removal of those falling within repetitive and phage regions (normally excluded for phylogenetic analysis).\




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