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Adding notes to CountCovariates docs about using interval lists as database of known variation

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Ryan Poplin 2012-01-17 16:13:13 -05:00
parent ae259f81cc
commit 8b0ddf0aaf
1 changed files with 3 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -155,7 +155,9 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
/////////////////////////////
/**
* This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites.
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of RodBindings (VCF, Bed, etc.)
* for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites.
* Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument.
*/
@Input(fullName="knownSites", shortName = "knownSites", doc="A database of known polymorphic sites to skip over in the recalibration algorithm", required=false)
public List<RodBinding<Feature>> knownSites = Collections.emptyList();