The alignment workflow starts with the fastq data and performs QC, aligns reads to the genome, remove duplicate reads and create coverage information.
- The base quality for fastq data
- All QC results
- Sample.genome.bam [.bai]
- Aligned bam files
- Sample.genome.dedup.bam [.bai]
- Aligned and deduplicated bam files, removing duplicated reads
- Showing the coverage at targeted regions.
Variant calling workflow
The variant calling workflow uses the prepared bam file from the alignment step to call the variants and annotate them.
- All variants in VCF format
- Mark dbSNP
- Add annotation to show the affected genes, amino acid change, etc.