Skip to content

Reads, calls and genes

You have aligned reads (a BAM with its .bai), variant calls (a VCF, gzipped or not) and an annotation (GFF3 or GTF).

karyon rpoB reads.bam genes.gff3 calls.vcf.gz -o rpoB.svg

The depth of the reads over the gene rpoB, the gene as an arrow, and seven calls as lollipops The same figure on the dark page

  • reads depth: how many reads cover each base. The dip is a stretch no read covers.
  • genes: each gene once, with its name and its direction.
  • calls: each variant at its position, as tall as its allele frequency, coloured by what the annotation says it does.

Change it

To Write
See the reads, not their depth --pileup reads.bam
See the bases, zoomed in NC_000962.3:761,100-761,200 --pileup reads.bam ref.fa
Draw a wider stretch NC_000962.3:755,000-770,000 in place of rpoB
Draw two genes, one under the other rpoB rpoC in place of rpoB
Make a row taller reads.bam --height 100
Rename a row calls.vcf.gz --label "variant calls"

The example files: reads.bam, reads.bam.bai, genes.gff3, calls.vcf.gz and ref.fa. Every option: karyon help coverage, or the command line reference.