Commit 0ffc7506 authored by Philip Mabon's avatar Philip Mabon

Merge branch 'doc/update-terminology' into 'development'

Doc/update terminology

See merge request !70
parents 1bb82b98 30662040
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......@@ -111,7 +111,7 @@ Once a proper paired-end dataset collection **ec-paired-reads** is constructed,
* **min_coverage**: 15
* **min_mean_mapping**: 30
* **alternative_allele_proportion (snv abundance ratio)**: 0.75
* **relative_snv_abundance (snv_abundance_ratio, or alternative_allele_proportion)**: 0.75
3. Verify that **Step 1: Input dataset collection** is set to **ec-paired-reads** that **Step 2: Input dataset** is set to **2011C-3609.fasta** and that **Step 3: Input dataset** is set to **invalid-positions.bed**.
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......@@ -99,7 +99,7 @@ Once a proper paired-end dataset collection **lm-paired-reads** is constructed,
* **min_coverage**: 15
* **min_mean_mapping**: 30
* **alternative_allele_proportion (snv abundance ratio)**: 0.75
* **relative_snv_abundance (snv_abundance_ratio, or alternative_allele_proportion)**: 0.75
![lm-run-parameters][]
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......@@ -15,7 +15,7 @@ The file `snvTable.tsv` represents a table of all detected variant sites. The p
* **valid**: Represents a position that passed all filtering criteria for every genome. These positions are used in the SNV alignment used to construct a phylogenetic tree and a distance matrix.
* **filtered-invalid**: Represents a position that was removed due to either being present on a repeat region, within a region with a high-SNV density, or within a region passed in the `invalid_positions` file.
* **filtered-coverage**: Represents a position where at least one genome did not meet the minimum coverage criteria. The value inserted in the table in this case is a `-`.
* **filtered-mpileup**: Represents a position where there was a mismatch in variant calls between **FreeBayes** and **SAMtools/mpileup/BCFtools**. This often occurs in positions which met the **min_coverage** criteria, but did not meet the other criteria for calling a variant with FreeBayes, such as the minimum snv abundance ratio (alternative allele ratio), or mapping quality scores. The value inserted in the table in this case is an `N`.
* **filtered-mpileup**: Represents a position where there was a mismatch in variant calls between **FreeBayes** and **SAMtools/mpileup/BCFtools**. This often occurs in positions which met the **min_coverage** criteria, but did not meet the other criteria for calling a variant with FreeBayes, such as the minimum relative snv abundance (snv abundance ratio, or alternative allele proportion), or mapping quality scores. The value inserted in the table in this case is an `N`.
![snv-table-galaxy][]
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......@@ -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 (alternative allele proportion)**: The proportion of reads required to support a variant to be included in the analysis. A reasonable value here is **0.75**.
3. **relative_snv_abundance (snv_abundance_ratio, or alternative_allele_proportion)**: 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_proportion** and **snv_abundance_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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