Coverage plots of gvcf files

Question

[Floris Brenk]

Hi all,

We have a bunch of gvcf files (400+) from exome data. What I would like to create coverage plots per exon, gene and/or genome wide. I know how to do this with bam files: like with depth of coverage of GATK and bedtools coverage hist, but cant find a way to do this with gvcf files. As far as I know the coverage information should be in the gvcf files.

I found this in GATK forum: http://gatkforums.broadinstitute.org/discussion/4315/depth-of-coverage-from-gvcf-files but I wouldnt know were to start scripting...

Does anyone has an idea or knows what the best way would be?

Thanks in advance...

[Sam]

Do you want the per sample depth or the average depth for each exon?

[Floris Brenk]

Both would be good to know in the end... But for now I'm interested in the average depth for each exon.