Stable
Detects SNPs and INDELs.
Inputs
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 |
Steps
ID | Name | Description |
---|---|---|
0 | List of Illumina accessions | |
1 | Refrence genome | |
2 | Reference genome annotation | COVID-19.gff |
3 | Illumina data | toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4 |
4 | SnpEff build: | toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy4 |
5 | fastp: Trimmed Illumina Reads | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
6 | Map with BWA-MEM | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 |
7 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 |
8 | Filter SAM or BAM, output SAM or BAM | toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8+galaxy1 |
9 | Illumina filtered reads | toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 |
10 | Bowtie2 | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
11 | AddOrReplaceReadGroups | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1 |
12 | SortSam | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1 |
13 | MarkDuplicates | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 |
14 | GATK4 Mutect2 | toolshed.g2.bx.psu.edu/repos/iuc/gatk4_mutect2/gatk4_mutect2/4.1.4.0+galaxy2 |
15 | VcfAllelicPrimitives: | toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc3+galaxy0 |
16 | SnpEff eff: | Annotate variants. toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 |
17 | SnpSift Extract Fields | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 |
18 | Concatenate datasets | cat1 |
Outputs
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 |

Creators
Not specifiedSubmitter
License
Activity
Views: 288 Downloads: 21
Created: 18th Jun 2020 at 16:49
Last used: 21st Jan 2021 at 15:05

None