VariantCaller_GATK3.6
Version 1

Stable

No description specified

SEEK ID: https://dev.workflowhub.eu/workflows/127?version=1

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

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

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