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Update docs of FastaAlternateReferenceMaker as promised in older GS thread

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Eric Banks 2012-08-01 10:33:41 -04:00
parent 687df2341d
commit a4a41458ef
1 changed files with 2 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
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@ -47,7 +47,8 @@ import java.util.List;
* <p> * <p>
* Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s). * Given variant tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
* Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'. * Additionally, allows for one or more "snpmask" VCFs to set overlapping bases to 'N'.
* Note that if there are multiple variants at a site, it takes the first one seen. * Note that if there are multiple variants at a site, it chooses one of them randomly.
* Also note that this tool works only for SNPs and for simple indels (but not for things like complex substitutions).
* Reference bases for each interval will be output as a separate fasta sequence (named numerically in order). * Reference bases for each interval will be output as a separate fasta sequence (named numerically in order).
* *
* <h2>Input</h2> * <h2>Input</h2>