Workflow Type: Galaxy

Detects SNPs and INDELs.


ID Name Description Type
bed_file bed_file runtime parameter for tool Filter SAM or BAM, output SAM or BAM n/a
intervals intervals runtime parameter for tool SnpEff eff: n/a
transcripts transcripts runtime parameter for tool SnpEff eff: n/a


ID Name Description
0 List of Illumina accessions
1 Refrence genome
2 Reference genome annotation COVID-19.gff
3 Illumina data
4 SnpEff build:
5 fastp: Trimmed Illumina Reads
6 Map with BWA-MEM
7 MultiQC
8 Filter SAM or BAM, output SAM or BAM
9 Illumina filtered reads
10 Bowtie2
11 AddOrReplaceReadGroups
12 SortSam
13 MarkDuplicates
14 GATK4 Mutect2
15 VcfAllelicPrimitives:
16 SnpEff eff: Annotate variants.
17 SnpSift Extract Fields
18 Concatenate datasets cat1


ID Name Description Type
list_paired list_paired n/a input
output_collection output_collection n/a input
output_collection_other output_collection_other n/a input
log log n/a txt
snpeff_output snpeff_output n/a snpeffdb
output_paired_coll output_paired_coll n/a input
report_html report_html n/a html
report_json report_json n/a json
bam_output bam_output n/a bam
stats stats n/a input
html_report html_report n/a html
output1 output1 n/a sam
forward forward n/a fasta
reverse reverse n/a fasta
output output n/a bam
mapping_stats mapping_stats n/a txt
outFile outFile n/a bam
outFile outFile n/a bam
metrics_file metrics_file n/a txt
outFile outFile n/a bam
output_vcf output_vcf n/a vcf
out_file1 out_file1 n/a vcf
snpeff_output snpeff_output n/a vcf
statsFile statsFile n/a html
output output n/a tabular
out_file1 out_file1 n/a input
help Creators and Submitter
Not specified

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Created: 18th Jun 2020 at 16:49

Last used: 6th Dec 2021 at 07:26

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Version 1 Created 18th Jun 2020 at 16:49 by Ambarish Kumar

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