GATK licensing moves to direct-through-Broad model -- read about it on the GATK blog

why does it say : -stand_call_conf: command not found while after running HaplotypeCaller

sunyunsunyun Posts: 8Member
edited June 2013 in Ask the GATK team

this is my script:

java -Xmx12g -jar /home/./programs/GenomeAnalysisTK.jar \
-R /home/./sas/hg19-1/ucsc.hg19.fasta \
-T HaplotypeCaller \
-I /share/users/./data/smu/step2/1.markDup.realign.recal.reduced.bam \
-I /share/users/./data/smu/step2/2.markDup.realign.recal.reduced.bam \
-stand_call_conf 30 \
-stand_emit_conf 0 \
–minPruning 3 \
–o /share/users/./data/smu/step2/1_2.withoutAnno.hap.vcf

Thank you !

Post edited by Geraldine_VdAuwera on

Best Answer


Sign In or Register to comment.