COVID-19: GATK4
Version 1

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
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Views: 217   Downloads: 14

Created: 18th Jun 2020 at 16:49

Last used: 26th Nov 2020 at 10:20

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