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.

Haplotype caller for RNA-seq

thkitapcithkitapci Los AngelesMember
edited September 2015 in Ask the GATK team

Hi,
I have been running HP for my RNA-seq data

java -Xmx16g -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $ref \
-I INPUT.bam \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-o output.vcf

my process is killed when it was 82% completed. Is there a way to resume the run without running from the beginning ?

Thanks
Best Regards
T. Hamdi Kitapci

Answers

Sign In or Register to comment.