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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