# HG changeset patch # User david-hoover # Date 1348161824 14400 # Node ID 642c7f54431a98d20d77357375b75c6718b02f85 # Parent 29507d31c174360b06f5eee4f79b7f12e99b2baf Uploaded diff -r 29507d31c174 -r 642c7f54431a base_recalibrator.xml --- a/base_recalibrator.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/base_recalibrator.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + on BAM files gatk diff -r 29507d31c174 -r 642c7f54431a depth_of_coverage.xml --- a/depth_of_coverage.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/depth_of_coverage.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + on BAM files gatk diff -r 29507d31c174 -r 642c7f54431a indel_realigner.xml --- a/indel_realigner.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/indel_realigner.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + - perform local realignment gatk diff -r 29507d31c174 -r 642c7f54431a print_reads.xml --- a/print_reads.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/print_reads.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + on BAM files gatk diff -r 29507d31c174 -r 642c7f54431a realigner_target_creator.xml --- a/realigner_target_creator.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/realigner_target_creator.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + for use in local realignment gatk diff -r 29507d31c174 -r 642c7f54431a unified_genotyper.xml --- a/unified_genotyper.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/unified_genotyper.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + SNP and indel caller gatk diff -r 29507d31c174 -r 642c7f54431a variant_annotator.xml --- a/variant_annotator.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_annotator.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk diff -r 29507d31c174 -r 642c7f54431a variant_apply_recalibration.xml --- a/variant_apply_recalibration.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_apply_recalibration.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk diff -r 29507d31c174 -r 642c7f54431a variant_combine.xml --- a/variant_combine.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_combine.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk diff -r 29507d31c174 -r 642c7f54431a variant_eval.xml --- a/variant_eval.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_eval.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk diff -r 29507d31c174 -r 642c7f54431a variant_filtration.xml --- a/variant_filtration.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_filtration.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + on VCF files gatk diff -r 29507d31c174 -r 642c7f54431a variant_recalibrator.xml --- a/variant_recalibrator.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_recalibrator.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk diff -r 29507d31c174 -r 642c7f54431a variant_select.xml --- a/variant_select.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variant_select.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + from VCF files gatk @@ -513,7 +513,7 @@ **What it does** -Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the Using JEXL expressions section (http://www.broadinstitute.org/gsa/wiki/index.php/Using_JEXL_expressions). One can optionally include concordance or discordance tracks for use in selecting overlapping variants. +Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP > 1000" (depth of coverage greater than 1000x), "AF < 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section <http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk>`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants. For more information on using the SelectVariants module, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html>`_. diff -r 29507d31c174 -r 642c7f54431a variants_validate.xml --- a/variants_validate.xml Thu Sep 20 12:03:32 2012 -0400 +++ b/variants_validate.xml Thu Sep 20 13:23:44 2012 -0400 @@ -1,4 +1,4 @@ - + gatk