Comments (3)
ilnamkang
commented on July 30, 2024
1
Thank you for your quick reply.
I've tested further.
The correct name of the option is "--bwa-parameters", not "--bwa-params".
This option seems to be available in "coverm make", but not in "coverm genome".
I was confused because this option is listed on the usage page of "coverm genome". (https://wwood.github.io/CoverM/coverm-genome.html)
For "coverm make", "--bwa-parameters -a" seems to work.
Thanks.
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wwood
commented on July 30, 2024
Hi,
Sorry I guess the documentation must be incorrect. I'm afk ATM so can't check properly, but maybe try
--bwa-parameters "'-a'"
You could also turn on debug so you know the right call is being made.
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