| 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. |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/variant_select
| Repository package_gatk_1_4 revision ec95ec570854 owned by devteam |
| Name | Version | Type | |
|---|---|---|---|
| gatk | 1.4 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| from VCF files | 0.0.3 | any | |