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In a recommended procedure in README, --mc 16 is set for runNanoSeq.py indel.
However, it causes an error runNanoSeq.py: error: unrecognized arguments: --mc 16.
Is the correct option for it -z?
P.S. extract-tags.py in README is a mistake for extract_tags.py.
The text was updated successfully, but these errors were encountered:
Sorry about that, the README needs a couple of updates, especially regarding the indel pipeline.
If you run runNanoSeq.py indel --help you will see that parameters have been changed:
optional arguments:
-h, --help show this help message and exit
-s SAMPLE, --sample SAMPLE
sample name in output vcf (sample_1)
--rb RB minimum reads in a bundle. (2)
--t3 T3 excess bases above this value are trimmed from 3'
(136)
--t5 T5 bases to trim from 5' reads (8)
-a A minimum AS-XS (50)
-c C fraction of clips (0.02)
-z Z minimum normal coverage (mc) (15)
-v V maximum normal VAF (0.01)
You are right -mc corresponds now to -z. We changed it to match the argument naming in the var command.
I hope this helps
In a recommended procedure in README,
--mc 16
is set for runNanoSeq.py indel.However, it causes an error
runNanoSeq.py: error: unrecognized arguments: --mc 16
.Is the correct option for it
-z
?P.S.
extract-tags.py
in README is a mistake forextract_tags.py
.The text was updated successfully, but these errors were encountered: