Calling variants in non-diploid systems
3.0

Workflow Type: Galaxy

Calling variants in non-diploid systems

Associated Tutorial

This workflows is part of the tutorial Calling variants in non-diploid systems, available in the GTN

Features

Thanks to...

Workflow Author(s): Anton Nekrutenko, Alex Ostrovsky

Tutorial Author(s): Anton Nekrutenko, Alex Ostrovsky

gtn star logo followed by the word workflows

Steps

ID Name Description
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
6 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
7 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
8 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1
9 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.19
10 MergeSamFiles toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/3.1.1.0
11 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
12 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.9
13 Filter BAM toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2
14 FreeBayes toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.9+galaxy0
15 VCFfilter: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc3+galaxy3
16 VCFtoTab-delimited: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc3+galaxy0
17 Cut Cut1

Version History

3.0 (earliest) Created 2nd Jun 2025 at 11:03 by GTN Bot

Added/updated 4 files


Open master a8dfb49
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
Activity

Views: 49   Downloads: 3   Runs: 0

Created: 2nd Jun 2025 at 11:03

help Attributions

None

Total size: 125 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH