NGS : Tuto SNP detection workflow single end
Created: 2014-03-04 14:21:37
Last updated: 2014-06-10 09:08:19
Generate pileup, Unify Genotypers and create a VCF file from FastQ files of two individuals
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Workflow Components
Inputs (4)
Name |
Description |
Fastq file from individual of first condition |
|
Fastq file from individual of second condition |
|
Input Dataset |
|
Input Dataset |
|
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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