Test MutectCaller

[PubuduSaneth]

MutectCaller testing

Test datasets

• Download testdata provided in Parabricks MutectCaller docs

Parabricks version and container

• Version: 4.7.0-1
• Docker image: docker://nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1
• Creating singularity image from docker - apptainer build clara-parabricks-4.7.0-1.sif docker://nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1

Test strategy

Parabricks command:

# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1 \
    pbrun mutectcaller \
    --ref /workdir/${REFERENCE_FILE} \
    --tumor-name <tumor_name_inside_bam_file> \
    --in-tumor-bam /workdir/${INPUT_TUMOR_BAM} \
    --in-normal-bam /workdir/${INPUT_NORMAL_BAM} \
    --normal-name <normal_name_inside_bam_file> \
    --out-vcf /outputdir/${OUTPUT_VCF}

Optional CLI arguments/parameters to test

• --num-gpus NUM_GPUS: Number of GPUs to use for a run. (default: 1)
• --run-partition: Turn on partition mode; divides genome into multiple partitions and runs 1 process per partition.
• --gpu-num-per-partition GPU_NUM_PER_PARTITION: Number of GPUs to use per partition.
• --num-htvc-threads NUM_HTVC_THREADS: Number of CPU threads per GPU to use. (default: 5)
• --in-tumor-recal-file IN_TUMOR_RECAL_FILE : Path of the report file after Base Quality Score Recalibration for tumor sample.
• --in-normal-recal-file IN_NORMAL_RECAL_FILE: Path of the report file after Base Quality Score Recalibration for normal sample.
• --pon PON : Path of the vcf.gz PON file. Make sure you run prepon first and there is a '.pon' file already.
• --mutect-germline-resource MUTECT_GERMLINE_RESOURCE: Path of the vcf.gz germline resource file. Population VCF of germline sequencing containing allele fractions.

[PubuduSaneth]

Singularity/Apptainer run command:

#!/bin/sh

REFERENCE_FILE="GCA_000001405.15_GRCh38_no_alt_analysis_set.fa"
INPUT_TUMOR_BAM="tumor.bam"
INPUT_NORMAL_BAM="normal.bam"
OUTPUT_VCF="tumor.mutectcaller.vcf"

TUMOR_NAME="COLO829BL_Ill_GSCPipe" # samtools view -H tumor.bam | grep "SM"
NORMAL_NAME="COLO829_Ill_GSCPipe" # samtools view -H normal.bam | grep "SM"

apptainer run --nv \
    --bind "$(pwd)":/workdir \
    --bind "$(pwd)":/outputdir \
    --pwd /workdir \
    clara-parabricks-4.7.0-1.sif \
    pbrun mutectcaller \
    --logfile mutectcaller.log \
    --ref /workdir/mutect_sample/${REFERENCE_FILE} \
    --tumor-name ${TUMOR_NAME}  \
    --in-tumor-bam /workdir/mutect_sample/${INPUT_TUMOR_BAM} \
    --in-normal-bam /workdir/mutect_sample/${INPUT_NORMAL_BAM} \
    --normal-name ${NORMAL_NAME} \
    --out-vcf /outputdir/mutect_sample/${OUTPUT_VCF}