zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update docs of FastaAlternateReferenceMaker as promised in older GS thread

This commit is contained in:
Eric Banks 2012-08-01 10:33:41 -04:00
parent 687df2341d
commit a4a41458ef
1 changed files with 2 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java
View File

@ -47,7 +47,8 @@ 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'.
* 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).
*
* <h2>Input</h2>