Parabricks haplotypecaller options

Healthcare & Life Sciences Parabricks
1

Hi, I am having trouble specifying --haplotypecaller-options.
How do you pass this argument?
I want to set the -standard-min-confidence-threshold-for-calling 20. But I can’t seem to get it to work. Documentation says pass it as a string. Can you give me an example?
I tried every possibility that I can think of.
eg: --haplotypecaller-options -standard-min-confidence-threshold-for-calling 20
–haplotypecaller -standard-min-confidence-threshold-for-calling 20
–haplotypecaller standard-min-confidence-threshold-for-calling 20

2

After reading another post, I tried setting it like this;

–haplotypecaller-options=-standard-min-confidence-threshold-for-calling 20

It gives me this error now.

pbrun: error: unrecognized arguments: 20

3

Hi nwijewardena,

Can you please try using :

–haplotypecaller-options=”-standard-min-confidence-threshold-for-calling 20”

As explained in the documentation :
https://docs.nvidia.com/clara/parabricks/v3.2/text/variant_callers.html#haplotypecaller

Best
Myrieme