created by Geraldine_VdAuwera
on 2019-07-14
This document is under construction. It aims to provide an overview of use cases covered by GATK Best Practices workflows.
Updated on 2019-07-14
From Aziz on 2019-08-02
Hi Geraldine,
I have used GATK for SNPcalling since 2016. I think when the last version released the old version did not work. I test both version but I got the same error.
The error copied below:
/var/spool/torque/mom_priv/jobs/4716059.brown-adm.rcac.purdue.edu.SC: line 24: GenomeAnalysisTK: command not found
my pipeline is:
GenomeAnalysisTK -nt 23 -T RealignerTargetCreator -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -o forIndelRealigner_JHIN01.intervals
GenomeAnalysisTK -T IndelRealigner -R branch_gene.fasta -I JHIN01_WG_aligned_dedup.bam -targetIntervals forIndelRealigner_JHIN01.intervals -o sorted_JHIN01_WG_aligned.bam
GenomeAnalysisTK -T HaplotypeCaller -R branch_gene.fasta -I sorted_JHIN01_WG_aligned.bam —emitRefConfidence GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -nct 23 -o variants_JHIN01_WG.g.vcf
From Aziz on 2019-08-02
I highly appreciate your help.