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fixed a typo in the string comment

This commit is contained in:
Yossi Farjoun 2012-09-05 14:46:10 -04:00
parent f4b39a7545
commit ad5fa449e7
1 changed files with 2 additions and 2 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -57,7 +57,7 @@ import java.util.TreeSet;
* is minimized across all the reads. In general, a large percent of regions requiring local realignment are due to the presence of an insertion
* or deletion (indels) in the individual's genome with respect to the reference genome. Such alignment artifacts result in many bases mismatching
* the reference near the misalignment, which are easily mistaken as SNPs. Moreover, since read mapping algorithms operate on each read independently,
* it is impossible to place reads on the reference genome such at mismatches are minimized across all reads. Consequently, even when some reads are
* it is impossible to place reads on the reference genome such that mismatches are minimized across all reads. Consequently, even when some reads are
* correctly mapped with indels, reads covering the indel near just the start or end of the read are often incorrectly mapped with respect the true indel,
* also requiring realignment. Local realignment serves to transform regions with misalignments due to indels into clean reads containing a consensus
* indel suitable for standard variant discovery approaches. Unlike most mappers, this walker uses the full alignment context to determine whether an
@ -69,7 +69,7 @@ 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.
* 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.
* <p>
* Another important note: 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.