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Preprocess input sequence files

• If the input sequences contain adaptors, use cutadapt or similar tools to trim them off.
• Use FastQC to access the quality of input sequences.

Align input suquences

1. Use bwa to align the sequences to reference genome.
2. Use Picard to sort and deduplicate the obtained alignment bam files.

Variant-call with GATK The preprocessing of bam files and variant-calling is conducted according to GATK best practices for DNAseq.

Annotate variants Evaluate the variants with Variant Effect Predictor or similar tools. Annotate the variants with allele frequencies in background population.

Run coverage analysis Use DepthOfCoverage from GATK to analyze coverage in the targeted regions.

Select and report variants Filter the variants according to criteria by requests (typical filters are functions, genomic context, frequencies.) Report the selected variants in VCF, BED or EXCEL format.