Workflow Type: Galaxy
Stable

Detects SNPs and INDELs.

Inputs

ID Name Description Type
List of Illumina accessions List of Illumina accessions n/a
  • File
Reference genome annotation Reference genome annotation COVID-19.gff
  • File
Refrence genome Refrence genome n/a
  • File

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
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File
_anonymous_output_17 _anonymous_output_17 n/a
  • File
_anonymous_output_18 _anonymous_output_18 n/a
  • File
_anonymous_output_19 _anonymous_output_19 n/a
  • File
_anonymous_output_20 _anonymous_output_20 n/a
  • File
VCF VCF n/a
  • File
_anonymous_output_21 _anonymous_output_21 n/a
  • File
_anonymous_output_22 _anonymous_output_22 n/a
  • File
_anonymous_output_23 _anonymous_output_23 n/a
  • File
_anonymous_output_24 _anonymous_output_24 n/a
  • File
_anonymous_output_25 _anonymous_output_25 n/a
  • File

Version History

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

Added/updated 2 files


Open master 27a22c7
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Views: 1383   Downloads: 55

Created: 18th Jun 2020 at 16:49

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