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Revision as of 17:21, 28 October 2014
, 17:21, 28 October 2014→Hard Filtering Options
==== Hard Filtering Options ====
==== Hard Filtering Options ====
These options set the values to use when applying hard filters.
* To remove any filter, set it to blank in your configuration file
'''Basic per variant filters:'''
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value
|-
| max depth || FILTER_MAX_SAMPLE_DP || rowspan="2" |INFO:DP || > ''conf value'' * total number of samples || 1000
|-
| min depth ||FILTER_MIN_SAMPLE_DP || < ''conf value'' * total number of samples || 1
|-
| rowspan="2"|number of samples with coverage || FILTER_MIN_NS_FRAC || rowspan="2" |INFO:NS || < ''conf value'' * total number of samples || .50
|-
| FILTER_MIN_NS || < ''conf value'' ||
|-
|}
'''Per variant filters that allow a range of values:'''
* values of these filters must be numbers (or comma/space separated list of numbers)
* Rules:
** Specifying 1 value in the filter will turn that filter on and use that value
** Specifying 2 values in the filter (separated by ',' and/or ' ') turns on the filter
*** Use the 1st value if the number of samples is below FILTER_FORMULA_MIN_SAMPLES
*** Use the 2nd value if the number of samples is above FILTER_FORMULA_MAX_SAMPLES
*** If the number of samples is between the MIN & MAX, a logscale is used:
***: <pre> (minVal - maxVal) * (log(maxSamples) - log(numSamples)) / (log(maxSamples) - log(minSamples)) + maxVal</pre>
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Program Description !! Default Value
! colspan="3" | Configuration settings for min/max # samples to determine filter value when the filter setting contains multiple values separated by ',' or ' '
|-
! Configuration Key !! Description !! Default Value
|-
| FILTER_FORMULA_MIN_SAMPLES || total number of samples < ''conf value'', use the value '''before''' the ',' or ' ' || 100
|-
| FILTER_FORMULA_MAX_SAMPLES || total number of samples > ''conf value'', use the value '''after''' the ',' or ' ' || 1000
|-
| colspan="3" | total number of samples between min & max, use logscale
|-
| colspan="3" |
|-
! colspan="3" | Filters
|-
|-
! Filter !! Configuration Key !! VCF value checked !! Filter Variants with... !! Default Value
|-
|-
|}
'''Additional VCF Cooker filters:'''
* If you want to add any additional VCF Cooker filters that don't already have a configuration item, you can do that by adding the vcfCooker command-line filter to GotCloud:
{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
! Configuration Key !! Default Value
|-
| FILTER_ADDITIONAL ||
|-
|}
|}
