QUALITY CONTROL (QC) METRICS
Accelerated CollectWGSMetrics functionality from GATK4
bammetrics collects whole genome sequencing metrics, similar to CollectWGSMetrics from GATK4, but in a highly accelerated manner. The output metrics match exactly with that of GATK4.
QUICK START
$ pbrun bammetrics --ref Ref.fa --bam wgs.bam --out-metrics-file metrics.txt
COMPATIBLE GATK4 COMMAND
The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will generate the exact same results as the output from the above command.
gatk CollectWGSMetrics -R Ref.fa -I wgs.bam -O metrics.txt
OPTIONS
- --ref
- --bam
- --out-metrics-file
- --minimum-base-quality
- --minimum-mapping-quality
- --count-unpaired
- --coverage-cap
- --num-threads
(required) Path to the reference file.
(required) Path to the input bam file.
(required) Output metrics file.
Minimum base quality for a base to contribute coverage (default: 20)
Minimum mapping quality for a read to contribute coverage (default: 20)
If true, count unpaired reads, and paired reads with one end unmapped (default: None)
Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED) (default: 250)
Defaults to 12.
Number of parallel threads to use.
Accelerated CollectMultipleMetrics from GATK4
collectmultiplemetrics collects whole genome sequencing metrics, similar to CollectMultipleMetrics from GATK4, but in a highly accelerated manner. The output metrics match exactly with that of GATK4.
QUICK START
CLI
$ pbrun collectmultiplemetrics --ref Ref.fa \
--bam wgs.bam \
--out-all-metrics metrics
COMPATIBLE GATK4 COMMAND
The command below is the GATK4 counterpart of the Parabricks command above. The output from these commands will generate the exact same results as the output from the above command.
gatk CollectMultipleMetrics --REFERENCE_SEQUENCE Ref.fa -I wgs.bam -O metrics \
--PROGRAM CollectAlignmentSummaryMetrics \
--PROGRAM CollectInsertSizeMetrics \
--PROGRAM QualityScoreDistribution \
--PROGRAM MeanQualityByCycle \
--PROGRAM CollectBaseDistributionByCycle \
--PROGRAM CollectGcBiasMetrics \
--PROGRAM CollectSequencingArtifactMetrics \
--PROGRAM CollectQualityYieldMetrics
OPTIONS
- --ref
- --bam
- --out-all-metrics
- --out-alignment
- --out-quality-score
- --out-insert-size
- --out-mean-quality-by-cycle
- --out-base-distribution-by-cycle
- --out-gc-bias
- --out-seq-artifact
- --out-quality-yield
- --processor-threads
- --bam-decompressor-threads
(required) Path to the reference file.
(required) Path to the input bam file.
Automatically run every analysis. The output Defaults to 8.file of each analysis will start with this prefix name. This is required if no individual metrics are specified.
Output file for alignment summary metric. This is not required if --out-all-metrics
is specified.
Output file for quality score distribution metric. This is not required if --out-all-metrics
is specified.
Output file for insert size metric. This is not required if --out-all-metrics
is specified.
Output file for mean quality by cycle metric. This is not required if --out-all-metrics
is specified.
Output file for base distribution by cycle metric. This is not required if --out-all-metrics
is specified.
Prefix name used to generate detail and summary files for gc bias metric. This is not required if --out-all-metrics
is specified.
Output file for sequencing artifact metric. This is not required if --out-all-metrics
is specified.
Output file for quality yield metric. This is not required if --out-all-metrics
is specified.
Defaults to 8.
Number of threads for processing (up to 20 threads shows increasing performance).
Defaults to 3.
Number of threads for bam decompression.