We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

HaplotypeCaller and reads mapped to multiple locations

xin.huangxin.huang Washington, DCMember

Dear GATK team,

I've been trying to use GATK to call SNPs from RNA-Seq data mapped to a transcriptome assembly. I used Bowtie2 for the read mapping. I apologize if the information is already posted, but it seemed hard to find out about this information, so I hoped to get some advice or pointed to the right place - How does the HaplotypeCaller handle reads mapped to multiple places? I used paired-end reads for read mapping.

Thank you very much for any feedback you might have.



Best Answer


Sign In or Register to comment.