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Markduplicates in Cram files. A valid CRAM reference was not supplied...
I wonder if you can help with the following. I am trying to mark duplicates in a cram file with the following command (picard latest):
'picard-tools MarkDuplicates I=09_1#21.cram O=09_1#21_md.cram M=09_1#21_md.txt'
I keep getting the following errors:
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalStateException: A valid CRAM reference was not supplied and one cannot be acquired via the property settings reference_fasta or use_cram_ref_download
I have also tried with the fasta reference R=in.fasta but nothing..
There is a similar post asking the same question but it doesn't seem to have been solved.
Many thanks in advance,