Calling variants in non-diploid systems

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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...

Tutorial Author(s): Anton Nekrutenko, Alex Ostrovsky

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1100?version=2

Inputs

ID Name Description Type
raw_child-ds-1.fq #main/raw_child-ds-1.fq n/a
  • File
raw_child-ds-2.fq #main/raw_child-ds-2.fq n/a
  • File
raw_mother-ds-1.fq #main/raw_mother-ds-1.fq n/a
  • File
raw_mother-ds-2.fq #main/raw_mother-ds-2.fq n/a
  • File

Steps

ID Name Description
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
6 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
7 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
8 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
9 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
10 MergeSamFiles toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1
11 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
12 BamLeftAlign toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0
13 Filter toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
14 FreeBayes toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0
15 VCFfilter: toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy3
16 VCFtoTab-delimited: toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0
17 Cut Cut1

Outputs

ID Name Description Type
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_11 #main/_anonymous_output_11 n/a
  • File
_anonymous_output_12 #main/_anonymous_output_12 n/a
  • File
_anonymous_output_13 #main/_anonymous_output_13 n/a
  • File
_anonymous_output_14 #main/_anonymous_output_14 n/a
  • File
_anonymous_output_15 #main/_anonymous_output_15 n/a
  • File
_anonymous_output_16 #main/_anonymous_output_16 n/a
  • File
_anonymous_output_17 #main/_anonymous_output_17 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File
cut_variants #main/cut_variants n/a
  • File

Version History

2.0 (latest) Created 16th Jul 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master dbfc97c

5.0 (earliest) Created 25th Jun 2024 at 10:57 by Helena Rasche

Added/updated 4 files


Frozen 5.0 68cdaeb
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
BWA
FreeBayes
BamTools
Vcflib
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Activity

Views: 1443   Downloads: 578   Runs: 0

Created: 25th Jun 2024 at 10:57

Last updated: 25th Jun 2024 at 10:57

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Total size: 107 KB
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