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Revision as of 15:51, 28 October 2014
, 15:51, 28 October 2014no edit summary
*''produce an error if reads overlap multiple targeted regions''
*''produce an error if reads overlap multiple targeted regions''
** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]]
** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]]
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| WGS_SVM || whether or not to run SVM on the whole genome rather than by chromosome (default is by chromosome). Set to TRUE if you are running with a small number of target regions. ||
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{| 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
! Configuration Key !! Program Description !! Default Value
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| WGS_SVM || whether or not to run SVM on the whole genome rather than by chromosome (default is by chromosome). Set to TRUE if you are running with a small number of target regions. ||
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| VCF_EXTRACT || position file to use for glfFlex ||
| VCF_EXTRACT || position file to use for glfFlex ||
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==== Options ====
==== Additional 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"
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| SAMTOOLS_VIEW_FILTER || filter settings for samtools view (default filters by mapping quality and flag) || -q 20 -F 0x0704
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| || WGS_SVM || ||
| NOBAQ_SUBSTRINGS || skip the BAQ step if the BAM filename contains the specified space-separated substrings || SOLID
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| || MAKE_OPTS || ||
| 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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| || KEEP_LOG || ||
| MAKE_OPTS || set to add additional makefile options ||
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