generic-variant-calling-wgs-pe/main
Version 1

Workflow Type: Galaxy

Generic variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff. The reference genome can be provided as a GenBank file.

Inputs

ID Name Description Type
Paired Collection Paired Collection Illumina reads with fastqsanger encoding n/a
GenBank genome GenBank genome GenBank with annotations for the genome of interest n/a
Name for genome database Name for genome database Should describe your reference genome, e.g. mpxv for Monkeypox virus. n/a
single_paired single_paired runtime parameter for tool fastp n/a
input_type input_type runtime parameter for tool SnpEff build: n/a
fastq_input fastq_input runtime parameter for tool Map with BWA-MEM n/a
reference_source reference_source runtime parameter for tool Map with BWA-MEM n/a
input input runtime parameter for tool Samtools view n/a
inputFile inputFile runtime parameter for tool MarkDuplicates n/a
reads reads runtime parameter for tool Realign reads n/a
reference_source reference_source runtime parameter for tool Realign reads n/a
input input runtime parameter for tool SnpEff eff: n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
snpDb snpDb runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a

Steps

ID Name Description
0 Paired Collection Illumina reads with fastqsanger encoding
1 GenBank genome GenBank with annotations for the genome of interest
2 Name for genome database Should describe your reference genome, e.g. mpxv for Monkeypox virus.
3 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
4 SnpEff build: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4
5 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2
6 Samtools view toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1
7 MarkDuplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
8 Samtools stats toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
9 Realign reads toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
10 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
11 Insert indel qualities toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
12 Call variants toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1
13 Lofreq filter toolshed.g2.bx.psu.edu/repos/iuc/lofreq_filter/lofreq_filter/2.1.5+galaxy0
14 SnpEff eff: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1

Outputs

ID Name Description Type
output_paired_coll output_paired_coll n/a
report_html report_html n/a
report_json report_json n/a
snpeff_output snpeff_output n/a
output_fasta output_fasta n/a
bam_output bam_output n/a
outputsam outputsam n/a
metrics_file metrics_file n/a
outFile outFile n/a
output output n/a
realigned realigned n/a
stats stats n/a
html_report html_report n/a
output output n/a
variants variants n/a
outvcf outvcf n/a
snpeff_output snpeff_output n/a
statsFile statsFile n/a

Version History

v0.1 (earliest) Created 4th Jun 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 10e094e
help Creators and Submitter
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Additional credit

Anton Nekrutenko

Submitter
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Views: 272

Created: 4th Jun 2022 at 03:01

Last used: 7th Dec 2022 at 09:20

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Total size: 1.01 MB
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