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.

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$ 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.

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gatk CollectWGSMetrics -R Ref.fa -I wgs.bam -O metrics.txt


OPTIONS

--ref

(required) Path to the reference file.

--bam

(required) Path to the input bam file.

--out-metrics-file

(required) Output metrics file.

--minimum-base-quality

Minimum base quality for a base to contribute coverage (default: 20)

--minimum-mapping-quality

Minimum mapping quality for a read to contribute coverage (default: 20)

--count-unpaired

If true, count unpaired reads, and paired reads with one end unmapped (default: None)

--coverage-cap

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)

--num-threads

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.

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CLI

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$ 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.

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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

(required) Path to the reference file.

--bam

(required) Path to the input bam file.

--out-all-metrics

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.

--out-alignment

Output file for alignment summary metric. This is not required if --out-all-metrics is specified.

--out-quality-score

Output file for quality score distribution metric. This is not required if --out-all-metrics is specified.

--out-insert-size

Output file for insert size metric. This is not required if --out-all-metrics is specified.

--out-mean-quality-by-cycle

Output file for mean quality by cycle metric. This is not required if --out-all-metrics is specified.

--out-base-distribution-by-cycle

Output file for base distribution by cycle metric. This is not required if --out-all-metrics is specified.

--out-gc-bias

Prefix name used to generate detail and summary files for gc bias metric. This is not required if --out-all-metrics is specified.

--out-seq-artifact

Output file for sequencing artifact metric. This is not required if --out-all-metrics is specified.

--out-quality-yield

Output file for quality yield metric. This is not required if --out-all-metrics is specified.

--processor-threads

Defaults to 8.

Number of threads for processing (up to 20 threads shows increasing performance).

--bam-decompressor-threads

Defaults to 3.

Number of threads for bam decompression.

© Copyright 2020, NVIDIA. Last updated on Sep 14, 2020.