Commit 1834d66a authored by Aaron Petkau's avatar Aaron Petkau

Added additional clarification

parent 9ef1931b
Pipeline #3950 passed with stage
in 11 seconds
......@@ -133,7 +133,7 @@ These parameters represent:
1. **min_coverage**: The minimum coverage for any given position on the reference genome to be included in the analysis. A reasonable value here is **10** or **15**.
2. **min_mean_mapping**: The minimum mean mapping quality score for all reads in a pileup to be included for analysis. A reasonable value here is **30**.
3. **snv_abundance_ratio (relative snv abundance)**: The proportion of reads required to support a variant to be included in the analysis. A reasonable value here is **0.75**.
3. **snv_abundance_ratio (relative snv abundance)**: The proportion of reads required to support a variant to be included in the analysis. A reasonable value here is **0.75**. This parameter has also been named **alternative allele ratio** in the past.
An additional parameter, **run_name**, is used to override the default name of datasets in the Galaxy workflow. This is not present in all versions of the SNVPhyl workflows.
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