Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

IndelRealigner results are different at time

Hello,

I use GATK v2.3 Lite.

I found that the output bam files generated by IndelRealigner from an input bam file were different at time.

There were only 4 realigned reads at a certain position at the first trial, but the realigned reads increased to 5 at the second trial.

Finally, it affected the variant calls.

Is there any random sampling process along the IndelRealigner ?

Could you explain more about the algorithm of IndelRealigner?

Thank you!

Tagged:

Answers

Sign In or Register to comment.