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Function: filters BAM file(s)
Usage: bamtools filter -in <BAM file> -out <BAM file> -length 100
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Function: Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
Usage: java -jar picard.jar CollectHiSeqXPfFailMetrics BASECALLS_DIR=/BaseCalls/ OUTPUT=/metrics/ LANE=001
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Function: Asserts the validity for specified Illumina basecalling data.
Usage: java -jar picard.jar CheckIlluminaDirectory BASECALLS_DIR=/BaseCalls/ READ_STRUCTURE=25T8B25T LANES=1 DATA_TYPES=BaseCalls
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Function: Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score recalibration (BQSR) if theoriginal qualities were retained.
Usage: java -jar picard.jar RevertSam I=input.bamO=reverted.bam
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Function: Converts a VCF or BCF file to a Picard Interval List.
Usage: java -jar picard.jar VcfToIntervalList
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Function: Collect metrics to quantify single-base sequencing artifacts.
Usage: java -jar picard.jar CollectSequencingArtifactMetrics I=input.bamO=artifact_metrics.txtR=reference_sequence.fasta
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Function: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
Usage: java -jar picard.jar CollectWgsMetrics I=input.bam O=collect_wgs_metrics.txt R=reference_sequence.fasta
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Function: Computes the depth at each position or region.
Usage: samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]]
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Function: Replace read groups in a BAM file.This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all reads to this read group in the OUTPUT BAM file.For more information about read groups, see the GATK Dictionary entry. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH) (see http://ga4gh.org/#/documentation).
Usage: java -jar picard.jar AddOrReplaceReadGroups I=input.bam O=output.bam RGID=4 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=20
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Function: Merge multiple BAM files into one
Usage: bamtools merge -in input_alignments_1.bam -in input_alignments_2.bam -in input_alignments_3.bam -out output_alignments_merged.bam
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Function: The command bamtools sort sorts a BAM file according to a given option. Output_alignments_sorted.bam is the resulting file, where the alignments are sorted by name.
Usage: bamtools sort -in input_alignments.bam -out output_alignments_sorted.bam -byname
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Function: prints number of alignments in BAM file(s)
Usage: bamtools count -in <BAM file>
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Function: Chart the nucleotide distribution per cycle in a SAM or BAM fileThis tool produces a chart of the nucleotide distribution per cycle in a SAM or BAM file in order to enable assessment of systematic errors at specific positions in the reads.
Usage: java -jar picard.jar CollectBaseDistributionByCycle CHART=collect_base_dist_by_cycle.pdf I=input.bam O=output.txt
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Function: Collect metrics about reads that pass quality thresholds and Illumina-specific filters. This tool evaluates the overall quality of reads within a bam file containing one read group. The output indicates the total numbers of bases within a read group that pass a minimum base quality score threshold and (in the case of Illumina data) pass Illumina quality filters as described in the GATK Dictionary entry.
Usage: java -jar picard.jar CollectQualityYieldMetrics I=input.bam O=quality_yield_metrics.txt \
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Function: Computes a number of metrics that are useful for evaluating coverage and performance of sequencing experiments.
Usage: java -jar picard.jar CollectWgsMetricsFromQuerySorted