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Merge pull request #74 from broadinstitute/eb_update_rtc_docs_GSA-716 

Update docs for RTC.
This commit is contained in:
Eric Banks 2013-02-27 11:58:09 -08:00
parent 97b332943b d2904cb636
commit 45fc0ed261
1 changed files with 5 additions and 2 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -91,9 +91,12 @@ import java.util.TreeSet;
* <li>Running the realigner over those intervals (see the IndelRealigner tool)</li>
* </ol>
* <p>
* An important note: the input BAM(s), reference, and known indel file(s) should be the same ones to be used for the IndelRealigner step.
* Important note 1: the input BAM(s), reference, and known indel file(s) should be the same ones to be used for the IndelRealigner step.
* <p>
* Another important note: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
* Important note 2: when multiple potential indels are found by the tool in the same general region, the tool will choose the most likely
* one for realignment to the exclusion of the others. This is a known limitation of the tool.
* <p>
* Important note 3: because reads produced from the 454 technology inherently contain false indels, the realigner will not currently work with them
* (or with reads from similar technologies). This tool also ignores MQ0 reads and reads with consecutive indel operators in the CIGAR string.
*
* <h2>Input</h2>