fq2bam - NVIDIA Docs

NVIDIA Docs Hub NVIDIA Clara Clara Parabricks 4.0.0 fq2bam

Generate BAM/CRAM output given one or more pairs of FASTQ files. Can also optionally generate a BQSR report.

fq2bam performs the following steps. The user can decide to turn-off marking of duplicates. The BQSR step is only performed if the --knownSites input and --out-recal-file output options are provided.

Quick Start

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            # This command assumes all the inputs are in 
 
   and all the outputs go to 
  
   .
  
 
$ docker run --rm --gpus all --volume <INPUT_DIR>:/workdir --volume <OUTPUT_DIR>:/outputdir
    -w /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
    pbrun fq2bam \
    --ref /workdir/${REFERENCE_FILE} \
    --in-fq /workdir/${INPUT_FASTQ_1} /workdir/${INPUT_FASTQ_2}  \
    --knownSites /workdir/${KNOWN_SITES_FILE} \
    --out-bam /outputdir/${OUTPUT_BAM} \
    --out-recal-file /outputdir/${OUTPUT_RECAL_FILE}

Compatible CPU-based BWA-MEM, GATK4 Commands

The commands below are the bwa-0.7.15 and GATK4 counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command. See the Output Comparison page for comparing the results.

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            # Run bwa-mem and pipe the output to create a sorted BAM.
$ bwa mem \
    -t 32 \
    -K 10000000 \
    -R '@RG\tID:sample_rg1\tLB:lib1\tPL:bar\tSM:sample\tPU:sample_rg1' \
    <INPUT_DIR>/${REFERENCE_FILE} <INPUT_DIR>/${INPUT_FASTQ_1} <INPUT_DIR>/${INPUT_FASTQ_2} | \
  gatk SortSam \
    --java-options -Xmx30g \
    --MAX_RECORDS_IN_RAM 5000000 \
    -I /dev/stdin \
    -O cpu.bam \
    --SORT_ORDER coordinate

# Mark duplicates.
$ gatk MarkDuplicates \
    --java-options -Xmx30g \
    -I cpu.bam \
    -O mark_dups_cpu.bam \
    -M metrics.txt

# Generate a BQSR report.
$ gatk BaseRecalibrator \
    --java-options -Xmx30g \
    --input mark_dups_cpu.bam \
    --output <OUTPUT_DIR>/${OUTPUT_RECAL_FILE} \
    --known-sites <INPUT_DIR>/${KNOWN_SITES_FILE} \
    --reference <INPUT_DIR>/${REFERENCE_FILE}

fq2bam Reference

Run GPU-bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration to convert FASTQ to BAM/CRAM.

Input/Output file options

--ref REF
--in-fq [IN_FQ [IN_FQ ...]]
--in-se-fq [IN_SE_FQ [IN_SE_FQ ...]]
--in-fq-list IN_FQ_LIST
--knownSites KNOWNSITES
--interval-file INTERVAL_FILE
--out-recal-file OUT_RECAL_FILE
--out-bam OUT_BAM
--out-duplicate-metrics OUT_DUPLICATE_METRICS
--out-qc-metrics-dir OUT_QC_METRICS_DIR

Tool Options:

-L INTERVAL, --interval INTERVAL
--bwa-options BWA_OPTIONS
--no-warnings
--no-markdups
--fix-mate
--markdups-assume-sortorder-queryname
--markdups-picard-version-2182
--optical-duplicate-pixel-distance OPTICAL_DUPLICATE_PIXEL_DISTANCE
--read-group-sm READ_GROUP_SM
--read-group-lb READ_GROUP_LB
--read-group-pl READ_GROUP_PL
--read-group-id-prefix READ_GROUP_ID_PREFIX
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Common options:

--logfile LOGFILE
--tmp-dir TMP_DIR
--with-petagene-dir WITH_PETAGENE_DIR
--keep-tmp
--no-seccomp-override
--version

GPU options:

--num-gpus NUM_GPUS

Note

The --in-fq option takes the names of two FASTQ files, optionally followed by a quoted read group. The FASTQ filenames must not start with a hyphen.

Note

When using the --in-fq-list option a read group is required on each line of the input file.