applybqsr

1
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
2
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
3
    --workdir /workdir \
4
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
5
    pbrun applybqsr \
6
    --ref /workdir/${REFERENCE_FILE} \
7
    --in-bam /workdir/${INPUT_BAM} \
8
    --in-recal-file /workdir/${INPUT_RECAL_FILE}  \
9
    --out-bam /outputdir/${OUTPUT_BAM}

1
$ gatk ApplyBQSR \
2
    --java-options -Xmx30g \
3
    -R <INPUT_DIR>/${REFERENCE_FILE} \
4
    -I <INPUT_DIR>/${INPUT_BAM} \
5
    --bqsr-recal-file <INPUT_DIR>/${INPUT_RECAL_FILE} \
6
    -O <OUTPUT_DIR>/${OUTPUT_BAM}