Mercurial > repos > david-hoover > garbage1
diff variant_select.xml @ 33:642c7f54431a draft default tip
Uploaded
author | david-hoover |
---|---|
date | Thu, 20 Sep 2012 13:23:44 -0400 |
parents | 29507d31c174 |
children |
line wrap: on
line diff
--- 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 @@ -<tool id="gatk2_variant_select" name="Select Variants" version="0.0.3"> +<tool id="gatk2_variant_select" name="Select Variants" version="0.0.4"> <description>from VCF files</description> <requirements> <requirement type="package" version="2.1">gatk</requirement> @@ -513,7 +513,7 @@ <help> **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>`_.