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Revision as of 13:49, 23 October 2014
, 13:49, 23 October 2014→INDEL VCF File(s)
=== INDEL VCF File(s) ===
=== INDEL VCF File(s) ===
VCF file containing OMNI positions
VCF file containing known INDEL positions
* Must be bgzip'd and tabix'd
* Must be bgzip'd and tabix'd
! Pipeline !! Use
! Pipeline !! Use
|-
|-
| snpcall || positive example sites for SVM filtering
| snpcall || used to filter variants that are too close to a known indel
|}
|}
* Use <code>INDEL_PREFIX</code> if <code>path/</code> contains a separate file for each chromosome in the format:<code>indels.sites.hg19.chr20.vcf</code> for each chromosome being processed
* Use <code>INDEL_VCF</code> if you have all chromosomes in a single VCF file (it can be, but does not have to be a gz file)
== Downloadable Reference and Resource Files ==
== Downloadable Reference and Resource Files ==
