VariantCaller_GATK3.6
Version 1

Stable

No description specified

Inputs

ID Name Description Type
library library runtime parameter for tool Cutadapt n/a
library library runtime parameter for tool Cutadapt n/a
reference_source reference_source runtime parameter for tool Map with BWA-MEM n/a
source source runtime parameter for tool gatk-RealignerTargetCreator n/a
source source runtime parameter for tool gatk-RealignerTargetCreator n/a
knownindels knownindels runtime parameter for tool gatk-RealignerTargetCreator n/a
source source runtime parameter for tool gatk-IndelRealigner n/a
source source runtime parameter for tool gatk-IndelRealigner n/a
known_sites known_sites runtime parameter for tool gatk-BaseRecalibrator n/a
source source runtime parameter for tool gatk-BaseRecalibrator n/a
source source runtime parameter for tool gatk-BaseRecalibrator n/a
source source runtime parameter for tool gatk-PrintReads n/a
source source runtime parameter for tool gatk-PrintReads n/a
source source runtime parameter for tool gatk-HaplotypeCaller n/a
source source runtime parameter for tool gatk-HaplotypeCaller n/a

Steps

ID Name Description
0 cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.6
1 BWA-MEM -> BAM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
2 picard-MarkDuplicates picard-MarkDuplicates
3 gatk-RealignerTargetCreator gatk-RealignerTargetCreator
4 gatk-IndelRealigner gatk-IndelRealigner
5 gatk-BaseRecalibrator gatk-BaseRecalibrator
6 gatk-PrintReads gatk-PrintReads
7 gatk-HaplotypeCaller gatk-HaplotypeCaller

Outputs

ID Name Description Type
split_output split_output n/a input
out1 out1 n/a fastqsanger
out2 out2 n/a fastqsanger
report report n/a txt
info_file info_file n/a txt
rest_output rest_output n/a fastqsanger
wild_output wild_output n/a txt
untrimmed_output untrimmed_output n/a fastqsanger
untrimmed_paired_output untrimmed_paired_output n/a fastqsanger
too_short_output too_short_output n/a fastqsanger
too_short_paired_output too_short_paired_output n/a fastqsanger
too_long_output too_long_output n/a fastqsanger
too_long_paired_output too_long_paired_output n/a fastqsanger
bam_output bam_output n/a bam
output output n/a bam
metrics metrics n/a txt
output output n/a interval
output output n/a bam
output output n/a table
output output n/a bam
output output n/a gvcf
help Creators and Submitter
Creator
  • Giacomo Tartari
Submitter
Activity

Views: 141   Downloads: 4

Created: 23rd Jul 2020 at 11:21

Last updated: 23rd Jul 2020 at 11:22

Last used: 20th Oct 2020 at 11:56

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