Step 1.5 eDiVA_prepare_for_annotation

Step 1.5 eDiVA_prepare_for_annotation

Once all samples from a family are processed and all variants have been called, this step takes care to perform the joint multisample calling of vairant positions, in order to gather all information for all samples.

nextflow run eDiVA_prepare_for_annotation.nf \
        --OUTF annotation/ \
        --FAMILY_INFO family_config \
        --CPU 2

Parameters

• OUTF : output folder
• CPU : number of CPU to use for the task
• FAMILY_INFO : it is a text file obtained by concatenating:
  • A header line with : "ID status vcf bam" separated by tab
  • The individual sample_info.txt of all samples, one per line.
  • It is important here to double check the text file to verify the AFFECTED column is correct, 0 for non-affected samples and 1 for the affected ones

Outputs

• VCF file with the multisample call : combined.variants.supplement.vcf
• Pedigree file for the next steps: pedigree.tree

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Docker execution

Provided you have edited nextflow.config as recommended adding volumes to the contained and prepared the family_config as suggested (using container paths, not local paths), the execution only requires ediva:code image

nextflow run eDiVA_prepare_for_annotation.nf \
        --OUTF annotation/ \
        --FAMILY_INFO family_config \
        --CPU 2 \
        -with_docker ediva:code

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Step 2-3 eDiVA-Annotate eDiVA-Score