Running alleleCounter with or without reference file
ilykos opened this issue · 1 comments
ilykos commented
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.
Deleted user commented
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.