Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Error in calculaitng DepthOfCoverage for a single BAM file

aditiskaditisk Ann Arbor Member

Hi,

I am trying to calculate the depthofcoverage for my samples as a prerequisite for running XHMM. When I provide a list of BAM files as the input it works just fine. But I am trying to make the calculation on a single BAM file and later I am trying to merge this read depth calculation to the calculations from 4 groups of 10 BAM files each. I am using the --mergeGATKdepths command from XHMM for merging my read depth files.

The error I am getting is as follows:
ERROR: Could not read any samples from /scratch/chadbren_flux/aditisk/Cell_Line_Characterization/XHMM/49710.sample_interval_statistics [expected suffix in header is: _mean_cvg]

Does depthofcoverage not support single BAM files as an input ?

Best Answer

Answers

Sign In or Register to comment.