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Mesh89 / TranSurVeyor

A transposition caller.
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usage for cram #4

Open jainy opened 3 years ago

jainy commented 3 years ago

Hi,

I would like to run Transurveyor for some of the cram files. Would it be possible to extend the usage for the cram file as well?

Thank you in advance Best, Jainy

Mesh89 commented 3 years ago

Hi,

Did you produce the CRAM yourself, or did you download them? If it's the former, there is a chance that it will work. I was able to run CRAMs, but the location of the reference genome should be stored in the CRAM.

jainy commented 3 years ago

Hi,

Thank you for the reply. I did not the produce the CRAM myself, I have downloaded from another server. So the reference file location in the cram won't be valid. Would it possible to give the new location of the reference genome as a command line option.

Thank you again for your support Best, Jainy

Mesh89 commented 3 years ago

Apologies for the delay.

I have plans to include proper cram support, but I will not have the time until probably early next year. For the moment, I am afraid the only way to use TranSurVeyor in your case would be to convert the files to bam.

jainy commented 3 years ago

Thank you! Looking forward to it!

Best, Jainy