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Eric Banks 2012-11-27 08:24:41 -05:00
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public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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@ -47,6 +47,12 @@ import java.util.List;
* <p>
* 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'.
*
* The output format can be partially controlled using the provided command-line arguments.
* Specify intervals with the usual -L argument to output only the reference bases within your intervals.
* Overlapping intervals are automatically merged; reference bases for each disjoint interval will be output as a
* separate fasta sequence (named numerically in order).
*
* Several important notes:
* 1) if there are multiple variants that start at a site, it chooses one of them randomly.
* 2) when there are overlapping indels (but with different start positions) only the first will be chosen.