bqsr

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

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$ gatk BaseRecalibrator \
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    --java-options -Xmx30g \
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    --input <INPUT_DIR>/${INPUT_BAM} \
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    --output <OUTPUT_DIR>/${INPUT_RECAL_FILE} \
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    --known-sites <INPUT_DIR>/${KNOWN_SITES_FILE} \
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    --reference <INPUT_DIR>/${REFERENCE_FILE}