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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

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