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Updating formating for ValidationAmplicons GATK docs

This commit is contained in:
Christopher Hartl 2011-09-15 21:05:51 -04:00
parent 9fdf1f8eb6
commit 939babc820
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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@ -61,7 +61,7 @@ import java.util.List;
* CACGTTCGGcttgtgcagagcctcaaggtcatccagaggtgatAGTTTAGGGCCCTCTCAAGTCTTTCCNGTGCGCATGG[GT/AC*]CAGCCCTGGGCACCTGTNNNNNNNNNNNNNTGCTCATGGCCTTCTAGATTCCCAGGAAATGTCAGAGCTTTTCAAAGCCC
*</pre>
* are amplicon sequences resulting from running the tool. The flags (preceding the sequence itself) can be:
*
*<pre>
* Valid // amplicon is valid
* SITE_IS_FILTERED=1 // validation site is not marked 'PASS' or '.' in its filter field ("you are trying to validate a filtered variant")
* VARIANT_TOO_NEAR_PROBE=1 // there is a variant too near to the variant to be validated, potentially shifting the mass-spec peak
@ -72,10 +72,10 @@ import java.util.List;
* END_TOO_CLOSE, // variant is too close to the end of the amplicon region to give sequenom a good chance to find a suitable primer
* NO_VARIANTS_FOUND, // no variants found within the amplicon region
* INDEL_OVERLAPS_VALIDATION_SITE, // an insertion or deletion interferes directly with the site to be validated (i.e. insertion directly preceding or postceding, or a deletion that spans the site itself)
* </p>
* </pre></p>
*
* <h2>Examples</h2>
* <pre></pre>
* <pre>
* java
* -jar GenomeAnalysisTK.jar
* -T ValidationAmplicons