Is it possible to extract Coverage track data to a table?

[jspai...@otogenetics.com]

I am trying to extract the Coverage track data including total count, breakdown of nucleotides, and forward/reverse read breakdown from the IGV interface.

This information appears in a pop up box when you hover over a column in the coverage track.

I am using v2.4.10 of the interface on a Windows 10 OS.  I have not used the command line version but i am not adverse to doing so if this would help.

I have tried using the count command in IGVtools with a  window size of one. This gives me a .wig file with the total count information per bp with out any of the breakdown. 

I have also tried using both samtools and bcftools with no success but any suggestions would be very helpful.

Is there another way to export this information into a table?  Is it also possible to take a larger file and export select ranges of the coverage information by referencing a .bed file?

Thank you, 

-John Spainhour

[James Robinson]

Look at the documentation for the command line igvtools,  there are flags for the count command to create ".wig" type files with the multiple columns.

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