Estimates the rate of independent replication rate of reads within a bam. That is, it estimates the fraction of the reads which would be marked as duplicates but are actually biological replicates, independent observations of the data.
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!)
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 | |
|---|---|---|---|
| Required Arguments | |||
| --INPUT -I |
null | Input (indexed) BAM file. | |
| --OUTPUT -O |
null | Write metrics to this file | |
| --VCF -V |
null | Input VCF file | |
| Optional Tool Arguments | |||
| --arguments_file |
[] | read one or more arguments files and add them to the command line | |
| --BARCODE_BQ |
QX | Barcode Quality SAM tag. | |
| --BARCODE_TAG |
RX | Barcode SAM tag. | |
| --help -h |
false | display the help message | |
| --MATRIX_OUTPUT -MO |
null | Write the confusion matrix (of UMIs) to this file | |
| --MINIMUM_BARCODE_BQ -MBQ |
30 | minimal value for the base quality of all the bases in a molecular barcode, for it to be used. | |
| --MINIMUM_BQ -BQ |
17 | minimal value for the base quality of a base to be used in the estimation. | |
| --MINIMUM_GQ -GQ |
90 | minimal value for the GQ field in the VCF to use variant site. | |
| --MINIMUM_MQ -MQ |
40 | minimal value for the mapping quality of the reads to be used in the estimation. | |
| --SAMPLE -ALIAS |
null | Name of sample to look at in VCF. Can be omitted if VCF contains only one sample. | |
| --STOP_AFTER |
0 | Number of sets to examine before stopping. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
| --CREATE_INDEX |
false | Whether to create a BAM index when writing a coordinate-sorted BAM file. | |
| --CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
| --GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
| --MAX_RECORDS_IN_RAM |
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. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --REFERENCE_SEQUENCE -R |
null | Reference sequence file. | |
| --TMP_DIR |
[] | 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 |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
| --USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
| --VALIDATION_STRINGENCY |
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. | |
| --VERBOSITY |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --showHidden |
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.
read one or more arguments files and add them to the command line
List[File] []
Barcode Quality SAM tag.
String QX
Barcode SAM tag.
String RX
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
Google Genomics API client_secrets.json file path.
String client_secrets.json
display the help message
boolean false
Input (indexed) BAM file.
R File null
Write the confusion matrix (of UMIs) to this file
File null
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 [ [ -∞ ∞ ] ]
minimal value for the base quality of all the bases in a molecular barcode, for it to be used.
Integer 30 [ [ -∞ ∞ ] ]
minimal value for the base quality of a base to be used in the estimation.
Integer 17 [ [ -∞ ∞ ] ]
minimal value for the GQ field in the VCF to use variant site.
Integer 90 [ [ -∞ ∞ ] ]
minimal value for the mapping quality of the reads to be used in the estimation.
Integer 40 [ [ -∞ ∞ ] ]
Write metrics to this file
R File null
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
File null
Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.
String null
display hidden arguments
boolean false
Number of sets to examine before stopping.
Integer 0 [ [ -∞ ∞ ] ]
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
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:
ValidationStringency STRICT
Input VCF file
R File null
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.0.11.0 built at 23-11-2018 02:11:49.