Estimates the rate of independent replication rate of reads within a bam.
This tool estimates the fraction of the input reads which would be marked as duplicates but are actually biological replicates, independent observations of the data.
The tools examines duplicate sets of size 2 and 3 that overlap known heterozygous sites of the sample. The tool classifies these duplicate sets into heterogeneous and homogeneous sets (those that contain the two alleles that are present in the variant and those that only contain one of them). From this the toolestimates the fraction of duplicates that arose from different original molecules, i.e. independently.
java -jar picard.jar CollectIndependentReplicateMetrics \ I=input.bam \ V=input.vcf \ O=output.independent_replicates_metrics \
Category Diagnostics and Quality Control
OverviewA CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam. That is, it estimates the fraction of the reads which look like duplicates (in the MarkDuplicates sense of the word) but are actually independent observations of the data. In the presence of Unique Molecular Identifiers (UMIs), various metrics are collected regarding the utility of the UMI's for the purpose of increasing coverage.
The estimation is based on duplicate-sets of size 2 and 3 and gives separate estimates from each. The assumption is that the duplication rate (biological or otherwise) is independent of the duplicate-set size. A significant difference between the two rates may be an indication that this assumption is incorrect.
The duplicate sets are found using the mate-cigar tag (MC) which is added by picard.sam.MergeBamAlignment , or picard.sam.FixMateInformation. This program will not work without the MC tag.
Explanation of the calculation behind the estimation can be found in the IndependentReplicateMetric class.
The calculation Assumes a diploid organism (more accurately, assumes that only two alleles can appear at a HET site and that these two alleles will appear at equal probabilities. It requires as input a VCF with genotypes for the sample in question. NOTE: This class is very much in alpha stage, and still under heavy development (feel free to join!)
CollectIndependentReplicateMetrics (Picard) specific arguments
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
|Argument name(s)||Default value||Summary|
|null||Input (indexed) BAM file.|
|null||Write metrics to this file|
|null||Input VCF file|
|Optional Tool Arguments|
||||read one or more arguments files and add them to the command line|
||QX||Barcode Quality SAM tag.|
||RX||Barcode SAM tag.|
|true||Whether to filter unpaired reads from the input.|
|false||display the help message|
|null||Write the confusion matrix (of UMIs) to this file|
|30||minimal value for the base quality of all the bases in a molecular barcode, for it to be used.|
|17||minimal value for the base quality of a base to be used in the estimation.|
|90||minimal value for the GQ field in the VCF to use variant site.|
|40||minimal value for the mapping quality of the reads to be used in the estimation.|
||100000||The interval between which progress will be displayed.|
|null||Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.|
||0||Number of sets to examine before stopping.|
||false||display the version number for this tool|
|Optional Common Arguments|
||5||Compression level for all compressed files created (e.g. BAM and VCF).|
||false||Whether to create a BAM index when writing a coordinate-sorted BAM file.|
||false||Whether to create an MD5 digest for any BAM or FASTQ files created.|
||client_secrets.json||Google Genomics API client_secrets.json file path.|
||500000||When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.|
||false||Whether to suppress job-summary info on System.err.|
|null||Reference sequence file.|
||||One or more directories with space available to be used by this program for temporary storage of working files|
|false||Use the JDK Deflater instead of the Intel Deflater for writing compressed output|
|false||Use the JDK Inflater instead of the Intel Inflater for reading compressed input|
||STRICT||Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.|
||INFO||Control verbosity of logging.|
||false||display hidden arguments|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
--arguments_file / NA
read one or more arguments files and add them to the command line
--BARCODE_BQ / NA
Barcode Quality SAM tag.
--BARCODE_TAG / NA
Barcode SAM tag.
--COMPRESSION_LEVEL / NA
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX / NA
Whether to create a BAM index when writing a coordinate-sorted BAM file.
--CREATE_MD5_FILE / NA
Whether to create an MD5 digest for any BAM or FASTQ files created.
--FILTER_UNPAIRED_READS / -FUR
Whether to filter unpaired reads from the input.
Google Genomics API client_secrets.json file path.
--help / -h
display the help message
--INPUT / -I
Input (indexed) BAM file.
R File null
--MATRIX_OUTPUT / -MO
Write the confusion matrix (of UMIs) to this file
--MAX_RECORDS_IN_RAM / NA
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
--MINIMUM_BARCODE_BQ / -MBQ
minimal value for the base quality of all the bases in a molecular barcode, for it to be used.
Integer 30 [ [ -∞ ∞ ] ]
--MINIMUM_BQ / -BQ
minimal value for the base quality of a base to be used in the estimation.
Integer 17 [ [ -∞ ∞ ] ]
--MINIMUM_GQ / -GQ
minimal value for the GQ field in the VCF to use variant site.
Integer 90 [ [ -∞ ∞ ] ]
--MINIMUM_MQ / -MQ
minimal value for the mapping quality of the reads to be used in the estimation.
Integer 40 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Write metrics to this file
R File null
The interval between which progress will be displayed.
int 100000 [ [ -∞ ∞ ] ]
--QUIET / NA
Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE / -R
Reference sequence file.
--SAMPLE / -ALIAS
Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.
--showHidden / -showHidden
display hidden arguments
--STOP_AFTER / NA
Number of sets to examine before stopping.
Integer 0 [ [ -∞ ∞ ] ]
--TMP_DIR / NA
One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
--VCF / -V
Input VCF file
R File null
--VERBOSITY / NA
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
--version / NA
display the version number for this tool
GATK version 18.104.22.168-SNAPSHOT built at Wed, 4 Mar 2020 13:47:07 -0500.