Skip to content

Commit

Permalink
Moved MQ0 out of HC exclusion and into StandardUGAnnotation
Browse files Browse the repository at this point in the history
  • Loading branch information
Geraldine Van der Auwera committed May 2, 2015
1 parent 8f31c71 commit fc890b6
Showing 1 changed file with 1 addition and 1 deletion.
Expand Up @@ -50,7 +50,7 @@
* <p>This annotation gives you the count of all reads that have MAPQ = 0 for each sample. The count of reads with MAPQ0 can be used for quality control; high counts typically indicate regions where it is difficult to make confident calls.</p>
*
* <h3>Caveat</h3>
* <p>This annotation is excluded by HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation would always return a value of 0 anyway.</p>
* <p>It is not useful to apply this annotation with HaplotypeCaller because HC filters out all reads with MQ0 upfront, so the annotation will always return a value of 0.</p>
*
* <h3>Related annotations</h3>
* <ul>
Expand Down

0 comments on commit fc890b6

Please sign in to comment.