Coverage

Note

The relevant data used in this tutorial is accessible at:

Warning

Make sure to download the relevant index file for each .bam (.bam.bai index), .cram (.cram.crai index), or .gz (.tbi index).

coverage

Let's retrieve the fragment number statistics (coverage), normalized (-n) for reads per million (--scale 1000000) from fragments that have a MAPQ score greater than 40 (-q 40), a minimum length of 25bp (-min 25), a maximum length of 250bp (-max 250) and whose have any overlap (-p any) on 100kb intervals across chromosome 22. We will output (-o) the BED to 100kb.22.coverage.bed, using one worker (-w 1) and verbose mode (-v).

finaletoolkit coverage \
    BH01.hg19.mdups.22.frag.gz \
    100kb.22.bins \
    -n \
    --scale 1e6 \
    -q 40 \
    -min 25 \
    -max 250 \
    -p any \
    -o 100kb.22.coverage.bed \
    -w 1 \
    -v

Our TSV output should look something like this:

22	19100000	19200000	.	2678.5778963551393
22	19200000	19300000	.	3217.2281910247116
22	19300000	19400000	.	3094.6388136171536
22	19400000	19500000	.	2847.2311610309916
22	19500000	19600000	.	3069.3779722119602