De Novo Calling

The De Novo Caller identifies all the trios within the pedigree and generate a de novo score for each child. The De Novo Caller supports multiple trios within a single pedigree. Pedigree Mode supports de novo calling for small, structural, and copy number variants.

Pedigree Mode is run in multiple steps. The following is an example workflow for a trio from FASTQ.

1.

Run single sample alignment and variant calling to generate per sample output using the following inputs for Pedigree Mode.

–

gVCF files for Small Variant Caller.

–

*.tn.tsv files for the Copy Number Caller.

–

BAM files for the Structural Variant Caller.

2.

Run Pedigree Mode for Small Variant Caller.

For more information, see Small Variant De Novo Calling.

3.

Run Pedigree Mode for Copy Number Caller.

For more information, see Multisample CNV Calling.

4.

Run Pedigree Mode for Structural Variant Caller.

For more information, see Structural Variant De Novo Quality Scoring.

5.

Run DeNovo Variant Small Variant Filtering.

For more information, see De Novo Small Variant Filtering.