diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java index a52d57031..b14dc9cc9 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java @@ -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; *
  • Running the realigner over those intervals (see the IndelRealigner tool)
  • * *

    - * 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. *

    * 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.