Clara Parabricks 4.0.0
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NVIDIA Clara Parabricks v4.0.0

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.

fq2bam.png

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

Path to the reference file. (default: None)

Option is required.
--in-fq [IN_FQ [IN_FQ ...]]

Path to the pair-ended FASTQ files followed by optional read groups with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:sampletPU:foo"). The files must be in fastq or fastq.gz format. All sets of inputs should have a read group; otherwise, none should have a read group, and it will be automatically added by the pipeline. This option can be repeated multiple times. Example 1: --in-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz --in-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz. Example 2: --in-fq sampleX_1_1.fastq.gz sampleX_1_2.fastq.gz "@RGtID:footLB:lib1tPL:bartSM:sampletPU:unit1" --in-fq sampleX_2_1.fastq.gz sampleX_2_2.fastq.gz "@RGtID:foo2tLB:lib1tPL:bartSM:sampletPU:unit2". For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU. (default: None)
--in-se-fq [IN_SE_FQ [IN_SE_FQ ...]]

Path to the single-ended FASTQ file followed by optional read group with quotes (Example: "@RGtID:footLB:lib1tPL:bartSM:sampletPU:foo"). The file must be in fastq or fastq.gz format. Either all sets of inputs have a read group, or none should have one, and it will be automatically added by the pipeline. This option can be repeated multiple times. Example 1: --in-se-fq sampleX_1.fastq.gz --in-se-fq sampleX_2.fastq.gz . Example 2: --in-se-fq sampleX_1.fastq.gz "@RGtID:footLB:lib1tPL:bartSM:sampletPU:unit1" --in-se-fq sampleX_2.fastq.gz "@RGtID:foo2tLB:lib1tPL:bartSM:sampletPU:unit2" . For the same sample, Read Groups should have the same sample name (SM) and a different ID and PU (default: None)
--in-fq-list IN_FQ_LIST

Path to a file that contains the locations of pair-ended FASTQ files followed by an optional read group, each separated by a space on the same line. Each set of pairs must be on a new line. Either all sets of inputs have a read group, or none should have one, and it will be automatically added by the pipeline. Files in the list must be in fastq/fastq.gz format. Line syntax: <fastq_1> <fastq_2> <optional read group> (default: None)
--knownSites KNOWNSITES

Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (default: None)
--interval-file INTERVAL_FILE

Path to an interval file in one of these formats: Picard-style (.interval_list or .picard), GATK-style (.list or .intervals), or BED file (.bed). This option can be used multiple times. (default: None)
--out-recal-file OUT_RECAL_FILE

Path of a report file after Base Quality Score Recalibration. (default: None)
--out-bam OUT_BAM

Path of a BAM/CRAM file after Marking Duplicates. (default: None)

Option is required.
--out-duplicate-metrics OUT_DUPLICATE_METRICS

Path of duplicate metrics file after Marking Duplicates. (default: None)
--out-qc-metrics-dir OUT_QC_METRICS_DIR

Path of the directory where QC metrics will be generated. (default: None)

Tool Options:

-L INTERVAL, --interval INTERVAL

Interval within which to call bqsr from the input reads. All intervals will have a padding of 100 to get read records, and overlapping intervals will be combined. Interval files should be passed using the --interval-file option. This option can be used multiple times (e.g. "-L chr1 -L chr2:10000 -L chr3:20000+ -L chr4:10000-20000") (default: None)
--bwa-options BWA_OPTIONS

Pass supported bwa mem options as one string. The current original bwa mem supported options are -M, -Y, and -T (e.g. --bwa-options="-M -Y") (default: None)
--no-warnings

Suppress warning messages about system thread and memory usage. (default: None)
--no-markdups

Do not perform the Mark Duplicates step. Return BAM after sorting. (default: None)
--fix-mate

Add mate cigar (MC) and mate quality (MQ) tags to the output file. (default: None)
--markdups-assume-sortorder-queryname

Assume the reads are sorted by queryname for Marking Duplicates. This will mark secondary, supplementary, and unmapped reads as duplicates as well. This flag will not impact variant calling while increasing processing times. (default: None)
--markdups-picard-version-2182

Assume marking duplicates to be similar to Picard version 2.18.2. (default: None)
--optical-duplicate-pixel-distance OPTICAL_DUPLICATE_PIXEL_DISTANCE

The maximum offset between two duplicate clusters in order to consider them optical duplicates. Ignored if --out-duplicate-metrics is not passed. (default: None)
--read-group-sm READ_GROUP_SM

SM tag for read groups in this run. (default: None)
--read-group-lb READ_GROUP_LB

LB tag for read groups in this run. (default: None)
--read-group-pl READ_GROUP_PL

PL tag for read groups in this run. (default: None)
--read-group-id-prefix READ_GROUP_ID_PREFIX

Prefix for the ID and PU tags for read groups in this run. This prefix will be used for all pairs of fastq files in this run. The ID and PU tags will consist of this prefix, and an identifier that will be unique for each pair of fastq files. (default: None)
-ip INTERVAL_PADDING, --interval-padding INTERVAL_PADDING

Amount of padding (in base pairs) to add to each interval you are including. (default: None)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.
--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)
--keep-tmp

Do not delete the directory storing temporary files after completion.
--no-seccomp-override

Do not override seccomp options for docker (default: None).
--version

View compatible software versions.

GPU options:

--num-gpus NUM_GPUS

Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.

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.


© Copyright 2022, Nvidia. Last updated on Jun 28, 2023.