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Revision as of 15:47, 28 October 2014
, 15:47, 28 October 2014→Options
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==== Options ====
==== GlfFlex Options ====
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{| 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
! Configuration Key !! Program Description !! Default Value
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| VCF_EXTRACT || position file to use for glfFlex ||
| || SAMTOOLS_VIEW_FILTER || ||
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|-
| || NOBAQ_SUBSTRINGS || skip the BAQ step if the BAM filename contains the specified space-separated substrings || SOLID
| MODEL_GLFSINGLE || set to TRUE if glfSingle model should be used for glfFlex ||
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|-
| || MODEL_GLFSINGLE || ||
| MODEL_SKIP_DISCOVER || set to true to disable variant discovery for glfFlex ||
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|-
| || MODEL_SKIP_DISCOVER || ||
| MODEL_AF_PRIOR || set to true to use AF prior for genotyping for glfFlex ||
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| || MODEL_AF_PRIOR || ||
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==== SVM Filtering Options ====
{| 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
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| || BAM_DEPEND || ||
| POS_SAMPLE || percentage of positive samples used for training || 100
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|-
| || WGS_SVM || ||
| NEG_SAMPLE || percentage of negative samples used for training || 100
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| || MAKE_OPTS || ||
| SVM_CUTOFF || SVM score cutoff for PASS/FAIL || 0
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| USE_SVMMODEL || whether to use pre-trained model for SVM filtering || FALSE
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| SVM_CUTOFF || ||
| SVMMODEL || pre-trained model file (if USE_SVMMODEL is set to TRUE) ||
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| SVMMODEL || ||
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==== Hard Filtering Options ====
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{| 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
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| FILTER_ADDITIONAL || ||
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==== Options ====
{| 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
|-
| || SAMTOOLS_VIEW_FILTER || filter settings for samtools view (default filters by mapping quality and flag) || -q 20 -F 0x0704
|-
| || NOBAQ_SUBSTRINGS || skip the BAQ step if the BAM filename contains the specified space-separated substrings || SOLID
|-
| || BAM_DEPEND || set to true to rerun the pipeline if the BAM files are newer than previously run steps that use them || FALSE
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| || WGS_SVM || ||
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| || MAKE_OPTS || ||
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| || KEEP_LOG || ||
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