NGS : Tuto SNP detection workflow single end

Created: 2014-03-04 14:21:37 Last updated: 2014-06-10 09:08:19

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Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals

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Inputs (4)

Steps (19)

Name	Tool	Description
Input dataset	None
Input dataset	None
Unified Genotyper	gatk_unified_genotyper
Generate pileup	toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.1
Unified Genotyper	gatk_unified_genotyper
Pileup-to-Interval	toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.0
Remove beginning	Remove beginning1
Convert Genomic Intervals To Strict BED6	CONVERTER_interval_to_bed6_0
Concatenate datasets	cat1
Filter	vcf_filter
Extract	vcf_extract
Input dataset	None
Input dataset	None
FASTQ Groomer	fastq_groomer
FASTQ Groomer	fastq_groomer
Bowtie2	bowtie2
Bowtie2	bowtie2
Add or Replace Groups	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0
Add or Replace Groups	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0

Outputs (23)

Name	Type
output_vcf	vcf
output_metrics	txt
output_log	txt
output1	tabular
output_vcf	vcf
output_metrics	txt
output_log	txt
output	tabular
out_file1	input
output1	bed6
out_file1	input
output1	vcf
output1	vcf
output_file	fastqsanger
output_file	fastqsanger
output_unaligned_reads_l	fastqsanger
output_unaligned_reads_r	fastqsanger
output	bam
output_unaligned_reads_l	fastqsanger
output_unaligned_reads_r	fastqsanger
output	bam
outFile	bam
outFile	bam

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Ylebras

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