Hi,

I am using GATK 4.1.7 and would like to use DepthOfCoverage to count fragments (--countType COUNT_FRAGMENTS in the older version).  However, the current beta version of DepthOfCoverage only allows COUNT_READS.  Will COUNT_FRAGMENTS be available in the final version, and when do you expect this might be released?

In the meantime, are there any other ways of getting this information?  I can't seem to use earlier versions of DepthOfCoverage on my CRAM files as I get the following error:

Command:

gatk -T DepthOfCoverage -I sample.cram -L intervals.interval_list -R genome.fa -o out

Error:

ERROR 2020-06-06 12:03:12 Slice Reference MD5 mismatch for slice 0:248639169-248877778, TGCAAAGAGA...ATAAGACCAG
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: SAM/BAM/CRAM file 1000144.cram is malformed. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1317for more information. Error details: Reference sequence MD5 mismatch for slice: sequence id 0, start 248639169, span 238610, expected MD5 357fd688ac5c67e21021d3595b1926de
##### ERROR ------------------------------------------------------------------------------------------

When I use the latest beta version, this works fine.

Thanks!

Kath