Export Coverage on IGV

Question

[callieboskin]

I have five different tracks on IGV from five sample alignment .bam files. I want to do more analysis on the coverage tracks that were made. Is there a way to export the coverage tracks from IGV into some file OR get the coverage at each individual point by some other method? Thank you!

[steve]

sounds like you might want to create a BigWig file? Also might want to look at GATK DepthOfCoverage (https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php)

Answer 1

[trausch]

We first create coverage tracks in UCSC bedgraph format using alfred

alfred tracks -o sample1.bedGraph.gz sample1.bam

and then you can use igvtools to convert the bedGraph files to IGV's proprietory tdf format.

igvtools totdf sample1.bedGraph.gz sample1.tdf hg19

You can then easily load several dozens of tdf files in IGV.

Answer 2

[WouterDeCoster]

Take a look at mosdepth, it's fast and most probably has the options you need

Answer 3

[ATpoint]

Use deeptools bamCoverage with -binsize set to 1 to get the per-base coverage. Lot of options for normalization etc available, see the documentation. Bigwigs can be readily loaded into IGV.