Coverage analysis for clinical sequencing

Simple Sambamba integration

There’s a new kid on the BAM processing block: Sambamba! You can easily load output into a Chanjo database for further coverage exploration:

$ sambamba depth region -L exons.bed -t 10 -t 20 alignment.bam > exons.coverage.bed
$ chanjo load exons.coverage.bed
$ chanjo calculate region 1 861321 871275 --sample ADM980A2
{"completeness_10": 100, "completeness_20": 87.123, "mean_coverage": 47.24234}

To learn more about Chanjo and how you can use it to gain a better understanding of sequencing coverage you can do no better than to:

Check out the demo

made by