Commit 9ef1931b authored by Aaron Petkau's avatar Aaron Petkau

Changed snv abundance ratio to relative snv abundance.

parent 1bb82b98
......@@ -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
* **alternative_allele_proportion (relative snv abundance)**: 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
* **alternative_allele_proportion (relative snv abundance)**: 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 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. **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**.
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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