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2016-11-06

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For the full documentation on how to use the gencore pipelines please see the gitbook.

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020_gatk_variant_filtration MAIN

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0.05
Jobname_001_bowtie2
Jobname_002_samtools_view
Jobname_003_picard_cleansam
Jobname_004_picard_sortsam
Jobname_005_remove_SAM
Jobname_006_samtools_sort
Jobname_007_picard_add_or_replace_groups
Jobname_008_picard_bamindex
Jobname_009_picard_collect_multiple_metrics
Jobname_010_picard_markdups
Jobname_011_samtools_mpileup
Jobname_012_tabix_index
Jobname_013_bcftools_filter
Jobname_014_bcftools_stats
Jobname_015_gatk_realigner_target_creator
Jobname_016_gatk_indel_realigner
Jobname_017_freebayes_vcf_calling
Jobname_018_freebayes_vcffilter
Jobname_019_gatk_haplotypecaller
Jobname_020_gatk_variant_filtration
Sample_5
SchedulerID_24590
SchedulerID_24591
SchedulerID_24592
SchedulerID_24593
SchedulerID_24594
SchedulerID_24595
SchedulerID_24596
SchedulerID_24597
SchedulerID_24598
SchedulerID_24599
SchedulerID_24600
SchedulerID_24601
SchedulerID_24602
SchedulerID_24603
SchedulerID_24604
SchedulerID_24605
SchedulerID_24606
SchedulerID_24607
SchedulerID_24608
SchedulerID_24609
compute-21-1.local
compute-21-4.local
gitbook
task_table

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0.05 Jobname_001_bowtie2 Jobname_002_samtools_view Jobname_003_picard_cleansam Jobname_004_picard_sortsam Jobname_005_remove_SAM Jobname_006_samtools_sort Jobname_007_picard_add_or_replace_groups Jobname_008_picard_bamindex Jobname_009_picard_collect_multiple_metrics Jobname_010_picard_markdups Jobname_011_samtools_mpileup Jobname_012_tabix_index Jobname_013_bcftools_filter Jobname_014_bcftools_stats Jobname_015_gatk_realigner_target_creator Jobname_016_gatk_indel_realigner Jobname_017_freebayes_vcf_calling Jobname_018_freebayes_vcffilter Jobname_019_gatk_haplotypecaller Jobname_020_gatk_variant_filtration Sample_5 SchedulerID_24590 SchedulerID_24591 SchedulerID_24592 SchedulerID_24593 SchedulerID_24594 SchedulerID_24595 SchedulerID_24596 SchedulerID_24597 SchedulerID_24598 SchedulerID_24599 SchedulerID_24600 SchedulerID_24601 SchedulerID_24602 SchedulerID_24603 SchedulerID_24604 SchedulerID_24605 SchedulerID_24606 SchedulerID_24607 SchedulerID_24608 SchedulerID_24609 compute-21-1.local compute-21-4.local gitbook task_table

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020_gatk_variant_filtration MAIN
020_gatk_variant_filtration CMD_020
019_gatk_haplotypecaller CMD_019 006
019_gatk_haplotypecaller CMD_019 005

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