The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

Haplotype caller for RNA-seq

thkitapcithkitapci Los AngelesMember
edited September 2015 in Ask the GATK team

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 ?

Best Regards
T. Hamdi Kitapci


Sign In or Register to comment.