Calculate statistics on fingerprints, checking their viabilityThis tools collects various statistics that pertain to a single fingerprint (not the comparison, or 'fingerprinting' of two distinct samples) and reports the results in a metrics file.
The statistics collected are p-values, where the null-hypothesis is that the fingerprint is collected from a non-contaminated, diploid human, whose genotypes are modelled by the probabilities given in the HAPLOTYPE_MAP file.
Please see the FingerprintMetrics definitions for a complete description of the metrics produced by this tool.
Example
" + java -jar picard.jar CalculateFingerprintMetrics \ INPUT=sample.bam \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ OUTPUT=sample.fingerprint_metrics
Category Diagnostics and Quality Control
Overview
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have. For example, if too many sites are heterozygous, that would get flagged.CalculateFingerprintMetrics (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 | |
---|---|---|---|
Required Arguments | |||
--HAPLOTYPE_MAP -H |
The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details. | ||
--INPUT -I |
One or more input files (SAM/BAM/CRAM or VCF). | ||
--OUTPUT -O |
The output file to write (Metrics). | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--CALCULATE_BY |
READGROUP | Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being used. Fingerprints from VCF can be be examined by SAMPLE or FILE. | |
--GENOTYPE_LOD_THRESHOLD |
3.0 | LOD score threshold for considering a genotype to be definitive. | |
--help -h |
false | display the help message | |
--NUMBER_OF_SAMPLING |
100 | Number of randomization trials for calculating the DISCRIMINATORY_POWER metric. | |
--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 an index when writing VCF or coordinate sorted BAM output. | |
--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 |
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 |
Argument details
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
read one or more arguments files and add them to the command line
List[File] []
--CALCULATE_BY
Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being used. Fingerprints from VCF can be be examined by SAMPLE or FILE.
The --CALCULATE_BY argument is an enumerated type (DataType), which can have one of the following values:
- FILE
- SAMPLE
- LIBRARY
- READGROUP
DataType READGROUP
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--GENOTYPE_LOD_THRESHOLD
LOD score threshold for considering a genotype to be definitive.
double 3.0 [ [ -∞ ∞ ] ]
--HAPLOTYPE_MAP / -H
The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.
R File null
--help / -h
display the help message
boolean false
--INPUT / -I
One or more input files (SAM/BAM/CRAM or VCF).
R List[String] []
--MAX_RECORDS_IN_RAM
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 [ [ -∞ ∞ ] ]
--NUMBER_OF_SAMPLING
Number of randomization trials for calculating the DISCRIMINATORY_POWER metric.
int 100 [ [ -∞ ∞ ] ]
--OUTPUT / -O
The output file to write (Metrics).
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--VALIDATION_STRINGENCY
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:
- STRICT
- LENIENT
- SILENT
ValidationStringency STRICT
--VERBOSITY
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
- ERROR
- WARNING
- INFO
- DEBUG
LogLevel INFO
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
0 comments
Please sign in to leave a comment.