Workflow Type: Galaxy
Open
Stable
Detects SNPs and INDELs.
Inputs
ID | Name | Description | Type |
---|---|---|---|
List of Illumina accessions | List of Illumina accessions | n/a |
|
Reference genome annotation | Reference genome annotation | COVID-19.gff |
|
Refrence genome | Refrence genome | n/a |
|
Steps
ID | Name | Description |
---|---|---|
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 |
---|---|---|---|
_anonymous_output_4 | _anonymous_output_4 | n/a |
|
_anonymous_output_5 | _anonymous_output_5 | n/a |
|
_anonymous_output_6 | _anonymous_output_6 | n/a |
|
_anonymous_output_7 | _anonymous_output_7 | n/a |
|
_anonymous_output_8 | _anonymous_output_8 | n/a |
|
_anonymous_output_9 | _anonymous_output_9 | n/a |
|
_anonymous_output_10 | _anonymous_output_10 | n/a |
|
_anonymous_output_11 | _anonymous_output_11 | n/a |
|
_anonymous_output_12 | _anonymous_output_12 | n/a |
|
_anonymous_output_13 | _anonymous_output_13 | n/a |
|
_anonymous_output_14 | _anonymous_output_14 | n/a |
|
_anonymous_output_15 | _anonymous_output_15 | n/a |
|
_anonymous_output_16 | _anonymous_output_16 | n/a |
|
_anonymous_output_17 | _anonymous_output_17 | n/a |
|
_anonymous_output_18 | _anonymous_output_18 | n/a |
|
_anonymous_output_19 | _anonymous_output_19 | n/a |
|
_anonymous_output_20 | _anonymous_output_20 | n/a |
|
VCF | VCF | n/a |
|
_anonymous_output_21 | _anonymous_output_21 | n/a |
|
_anonymous_output_22 | _anonymous_output_22 | n/a |
|
_anonymous_output_23 | _anonymous_output_23 | n/a |
|
_anonymous_output_24 | _anonymous_output_24 | n/a |
|
_anonymous_output_25 | _anonymous_output_25 | n/a |
|
Version History
Version 1 (earliest) Created 18th Jun 2020 at 16:49 by Ambarish Kumar
Added/updated 2 files
Open
master
27a22c7