Running alleleCounter with or without reference file

Question

Running alleleCounter with or without reference file

ilykos opened this issue 5 years ago · 1 comments

ilykos commented 5 years ago

Hi,

I may have missed this, but providing "reference file" (-r flag) is marked as optional in the help section.

Are there any advantages/disadvantages of providing reference file to alleleCounter?

Thanks.

Answer 1 · 2019-07-11T14:14:46.000Z

The reference file option was mainly provided for use when giving CRAM as input in case the reference was not embedded in the CRAM file. Using BAM you should see no difference.