Input dataset
output
Input dataset
output
Input dataset
output
Input dataset
output
FASTQ Groomer
File to groom
output_file
FASTQ Groomer
File to groom
output_file
Bowtie2
FASTQ file
output_unaligned_reads_l
output_unaligned_reads_r
output
Bowtie2
FASTQ file
output_unaligned_reads_l
output_unaligned_reads_r
output
Add or Replace Groups
SAM/BAM dataset to add or replace read groups in
outFile
Add or Replace Groups
SAM/BAM dataset to add or replace read groups in
outFile
Unified Genotyper
BAM file 1 > BAM file
Using reference file
output_vcf
output_metrics
output_log
Generate pileup
Select the BAM file to generate the pileup file for
Select a reference genome
output1
Unified Genotyper
BAM file 1 > BAM file
Using reference file
output_vcf
output_metrics
output_log
Pileup-to-Interval
Choose a pileup file to condense:
output
Remove beginning
from
out_file1
Convert Genomic Intervals To Strict BED6
Choose intervals
output1
Concatenate datasets
Concatenate Dataset
Dataset 1 > Select
out_file1
Filter
VCF file
output1
Extract
VCF file
output1