Question: Coverage plots of gvcf files
0
gravatar for Floris Brenk
5.4 years ago by
Floris Brenk950
USA
Floris Brenk950 wrote:

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...

gvcf coverage gatk exome • 2.2k views
ADD COMMENTlink written 5.4 years ago by Floris Brenk950

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

ADD REPLYlink written 5.4 years ago by Sam3.2k

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

ADD REPLYlink written 5.4 years ago by Floris Brenk950
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