Linux / amd64
Annotate variants based on a PON file and modify the "INFO" field of the input VCF file. This is the post process step of using --pon in mutect.
For further information visit the postpon help page.
# This command assumes all the inputs are in <INPUT_DIR> and all the outputs go to <OUTPUT_DIR>.
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
-w /workdir \
nvcr.io/nvidia/clara/clara-parabricks:<VERSION-TAG> \
pbrun postpon \
--in-vcf /workdir/${INPUT_VCF} \
--in-pon-file /workdir/${INPUT_PON_VCF} \
--out-vcf /outputdir/${OUTPUT_VCF}