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Fix tagging syntax 

Syntax was given as -V:format,name but should be -V:name,format
This commit is contained in:
Geraldine Van der Auwera 2016-05-17 08:42:49 -04:00
parent 81a67d67f7
commit 6d5b643a9d
1 changed files with 4 additions and 4 deletions
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8
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineVariants.java
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@ -72,9 +72,9 @@ import java.util.*;
* </ul>
*
* <p>By default, the input sets will be named variants, variants2, variants3, and so on. You can override this by
* providing an explicit name tag for each input, using the syntax " -V:format,name". Each input tagged in this
* providing an explicit name tag for each input, using the syntax " -V:name,format". Each input tagged in this
* way will be labeled as such in the output (i.e., set=name rather than set=variants2). For example, you could specify
* a set of control samples as " -V:vcf,control my_control_samples.vcf", and the resulting VCF records would contain
* a set of control samples as " -V:control,vcf my_control_samples.vcf", and the resulting VCF records would contain
* the annotation "set=control" in the INFO field. It is strongly recommended to provide explicit names in this way
* when a rod priority list is provided.</p>
*
@ -123,8 +123,8 @@ import java.util.*;
*
* <h3>Caveats</h3>
* <ul>
* <li>This tool is not intended to manipulate GVCFS! To combine GVCF files output by HaplotypeCaller, use CombineGVCFs.</li>
* <li>To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome), use CatVariants.</li>
* <li>This tool is not intended to manipulate GVCFS! To combine GVCF files output for different samples by HaplotypeCaller, use CombineGVCFs.</li>
* <li>To join intermediate VCFs produced by running jobs in parallel by interval (e.g. by chromosome) from the same sample, use CatVariants.</li>
* </ul>
*
* <h3>Additional notes</h3>