GBS-based SNPs filtering and imputation


StepAnnotation
Step 1: Input dataset
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Step 2: Input dataset
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Step 3: Input dataset
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Step 4: Input dataset
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Step 5: Input dataset
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Step 6: Input dataset
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Step 7: CornellVCFStandardization
Output dataset 'output' from step 1
Output dataset 'output' from step 2
Step 8: Individual missingness filter
Output dataset 'vcf_ouput' from step 7
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No value found for 'Reference fasta file'. Using default: ''.

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Step 9: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0'
Step 10: VCFtools Filter
select at runtime

No value found for 'VCF input'. Using default: ''.

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Step 11: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_annotator/2.8.0'
Step 12: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0'
Step 13: Read depth filter
Output dataset 'output_vcf' from step 12
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Step 14: Beagle
Output dataset 'vcf_ouput' from step 13
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Step 15: phasedVCFtoHapMap
Output dataset 'vcf_ouput' from step 14
Step 16: Tassel
Output dataset 'hapmap_output' from step 15
MLM
Output dataset 'output' from step 4
Output dataset 'output' from step 5
yes
Output dataset 'output' from step 6
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