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Error in calculaitng DepthOfCoverage for a single BAM file

aditiskaditisk Ann Arbor Member


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


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