Alignment workflow
The alignment workflow starts with the fastq data and performs QC, aligns reads to the genome, remove duplicate reads and create coverage information.
-
Sample.trimmed.per-base-quality.png - The base quality for fastq data
- Sample.trimmed_fastqc.zip
- All QC results
- Sample.genome.bam [.bai]
- Aligned bam files
- Sample.genome.dedup.bam [.bai]
- Aligned and deduplicated bam files, removing duplicated reads
- Sample.genome.dedup.coverage-plot.png
- 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.
-
Sample.genome.variants.vcf - All variants in VCF format
- Sample.genome.variants.marked.vcf
- Mark dbSNP
- Sample.genome.variants.marked.annotated.vcf
- Add annotation to show the affected genes, amino acid change, etc.