zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added note of caution to VQSR gatkdocs for option BOTH of recalibration mode

This commit is contained in:
Geraldine Van der Auwera 2013-07-23 13:27:47 -04:00
parent f52196496d
commit edbd17b8e0
1 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
View File

@ -70,9 +70,9 @@ public class VariantRecalibratorArgumentCollection {
throw new ReviewedStingException("VariantRecalibrator mode string is unrecognized, input = " + input);
}
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only snps (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both snps and indels simultaneously.", required = false)
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels (emitting SNPs untouched in the output VCF); and 3.) BOTH for recalibrating both SNPs and indels simultaneously (for testing purposes only, not recommended for general use).", required = false)
public VariantRecalibratorArgumentCollection.Mode MODE = VariantRecalibratorArgumentCollection.Mode.SNP;
@Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm", required=false)
@Argument(fullName="maxGaussians", shortName="mG", doc="The maximum number of Gaussians to try during variational Bayes algorithm.", required=false)
public int MAX_GAUSSIANS = 10;
@Argument(fullName="maxIterations", shortName="mI", doc="The maximum number of VBEM iterations to be performed in variational Bayes algorithm. Procedure will normally end when convergence is detected.", required=false)
public int MAX_ITERATIONS = 100;