why does it say : -stand_call_conf: command not found while after running HaplotypeCaller
Posted in Ask the GATK team | Last updated on 2013-06-14 00:31:33


Comments (2)

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 !


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