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.
$ pbrun fq2bam \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-fq Data/sample_1.fq.gz Data/sample_2.fq.gz \
--knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--out-bam mark_dups_gpu.bam \
--out-recal-file recal_gpu.txt \
--tmp-dir /raid/myrun
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.
# Run bwa-mem and pipe output to create sorted BAM
$ bwa mem -t 32 -K 10000000 -R '@RG\tID:sample_rg1\tLB:lib1\tPL:bar\tSM:sample\tPU:sample_rg1' \
Ref/Homo_sapiens_assembly38.fasta Data/sample_1.fq.gz Data/sample_2.fq.gz | gatk \
SortSam --java-options -Xmx30g --MAX_RECORDS_IN_RAM=5000000 -I=/dev/stdin \
-O=cpu.bam --SORT_ORDER=coordinate --TMP_DIR=/raid/myrun
# Mark Duplicates
$ gatk MarkDuplicates --java-options -Xmx30g -I=cpu.bam -O=mark_dups_cpu.bam \
-M=metrics.txt --TMP_DIR=/raid/myrun
# Generate BQSR Report
$ gatk BaseRecalibrator --java-options -Xmx30g --input mark_dups_cpu.bam --output \
recal_cpu.txt --known-sites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz \
--reference Ref/Homo_sapiens_assembly38.fasta
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
Path to the reference file. (default: None)
Option is required.
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)
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 read group or none should have it and 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)
Path to a file that contains the locations of pair-ended FASTQ files followed by 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 read group or none should have it and 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)
Path to a known indels file. The file must be in vcf.gz format. This option can be used multiple times. (default: None)
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)
Path of a report file after Base Quality Score Recalibration. (default: None)
Path of a BAM/CRAM file after Marking Duplicates. (default: None)
Option is required.
Path of duplicate metrics file after Marking Duplicates. (default: None)
Path of the directory where QC metrics will be generated. (default: None)
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
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)
Pass supported bwa mem options as one string. The current original bwa mem supported options are -M, -Y, -T (e.g. --bwa-options="-M -Y") (default: None)
Suppress warning messages about system thread and memory usage. (default: None)
Do not perform the Mark Duplicates step. Return BAM after sorting. (default: None)
Add mate cigar (MC) and mate quality (MQ) tags to the output file. (default: None)
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)
Assume marking duplicates to be similar to Picard version 2.18.2. (default: None)
The maximum offset between two duplicate clusters in order to consider them optical duplicates. Ignored if --out-duplicate-metrics is not passed. (default: None)
SM tag for read groups in this run. (default: None)
LB tag for read groups in this run. (default: None)
PL tag for read groups in this run. (default: None)
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 a pair of fastq files. (default: None)
Amount of padding (in base pairs) to add to each interval you are including. (default: None)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.
GPU options:
- --num-gpus NUM_GPUS
- --gpu-devices GPU_DEVICES
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
GPU devices to use for a run. By default, all GPU devices will be used.
To use specific GPU devices, enter a comma-separated list of GPU device
numbers. Possible device numbers can be found by examining the output of
the nvidia-smi command. For example, using --gpu-devices 0,1
would only use the first two GPUs.
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.