collectmultiplemetrics

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

Option

Description

--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.