DEPRECATED: USE CrosscheckFingerprints. Checks if all read groups within a set of BAM files appear to come from the same individual
Category Diagnostics and Quality Control
Overview
Program to check that all read groups within the set of BAM files appear to come from the same individual.CrosscheckReadGroupFingerprints (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 |
null | 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 (or lists of files) with which to compare fingerprints. | |
Optional Tool Arguments | |||
--ALLOW_DUPLICATE_READS |
false | Allow the use of duplicate reads in performing the comparison. Can be useful when duplicate marking has been overly aggressive and coverage is low. | |
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--CALCULATE_TUMOR_AWARE_RESULTS |
true | specifies whether the Tumor-aware result should be calculated. These are time consuming and can roughly double the runtime of the tool. When crosschecking many groups not calculating the tumor-aware results can result in a significant speedup. | |
--CROSSCHECK_BY |
READGROUP | Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE. | |
--CROSSCHECK_LIBRARIES |
false | Instead of producing the normal comparison of read-groups, roll fingerprints up to the library level and print out a library x library matrix with LOD scores. | |
--CROSSCHECK_MODE |
CHECK_SAME_SAMPLE | An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. | |
--CROSSCHECK_SAMPLES |
false | Instead of producing the normal comparison of read-groups, roll fingerprints up to the sample level and print out a sample x sample matrix with LOD scores. | |
--EXIT_CODE_WHEN_MISMATCH |
1 | When one or more mismatches between groups is detected, exit with this value instead of 0. | |
--EXPECT_ALL_GROUPS_TO_MATCH |
false | Expect all groups' fingerprints to match, irrespective of their sample names. By default (with this value set to false), groups (readgroups, libraries, files, or samples) with different sample names are expected to mismatch, and those with the same sample name are expected to match. | |
--EXPECT_ALL_READ_GROUPS_TO_MATCH |
false | Expect all read groups' fingerprints to match, irrespective of their sample names. By default (with this value set to false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected to match. | |
--GENOTYPING_ERROR_RATE |
0.01 | Assumed genotyping error rate that provides a floor on the probability that a genotype comes from the expected sample. Must be greater than zero. | |
--help -h |
false | display the help message | |
--INPUT_SAMPLE_MAP |
null | A tsv with two columns representing the sample as it appears in the INPUT data (in column 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT. | |
--LOD_THRESHOLD -LOD |
0.0 | If any two groups (with the same sample name) match with a LOD score lower than the threshold the tool will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD. LOD score 0 means equal likelihood that the groups match vs. come from different individuals, negative LOD score -N, mean 10^N time more likely that the groups are from different individuals, and +N means 10^N times more likely that the groups are from the same individual. | |
--LOSS_OF_HET_RATE |
0.5 | The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via loss of heterozygosity) in the tumor (model assumes independent events, so this needs to be larger than reality). | |
--MATRIX_OUTPUT -MO |
null | Optional output file to write matrix of LOD scores to. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Heterozygosity). It is however sometimes easier to use visually. | |
--NUM_THREADS |
1 | The number of threads to use to process files and generate fingerprints. | |
--OUTPUT -O |
null | Optional output file to write metrics to. Default is to write to stdout. | |
--OUTPUT_ERRORS_ONLY |
false | If true then only groups that do not relate to each other as expected will have their LODs reported. | |
--SECOND_INPUT -SI |
[] | A second set of input files (or lists of files) with which to compare fingerprints. If this option is provided the tool compares each sample in INPUT with the sample from SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool will proceed to check the matching samples, but report the missing samples and return a non-zero error-code. | |
--SECOND_INPUT_SAMPLE_MAP |
null | A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in column 1) and the sample as it should be used for comparisons to INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT. | |
--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 |
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.
--ALLOW_DUPLICATE_READS / NA
Allow the use of duplicate reads in performing the comparison. Can be useful when duplicate marking has been overly aggressive and coverage is low.
boolean false
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--CALCULATE_TUMOR_AWARE_RESULTS / NA
specifies whether the Tumor-aware result should be calculated. These are time consuming and can roughly double the runtime of the tool. When crosschecking many groups not calculating the tumor-aware results can result in a significant speedup.
boolean true
--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.
Boolean false
--CREATE_MD5_FILE / NA
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--CROSSCHECK_BY / NA
Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE.
The --CROSSCHECK_BY argument is an enumerated type (DataType), which can have one of the following values:
- FILE
- SAMPLE
- LIBRARY
- READGROUP
DataType READGROUP
--CROSSCHECK_LIBRARIES / NA
Instead of producing the normal comparison of read-groups, roll fingerprints up to the library level and print out a library x library matrix with LOD scores.
boolean false
--CROSSCHECK_MODE / NA
An argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur.
The --CROSSCHECK_MODE argument is an enumerated type (CrosscheckMode), which can have one of the following values:
- CHECK_SAME_SAMPLE
- CHECK_ALL_OTHERS
CrosscheckMode CHECK_SAME_SAMPLE
--CROSSCHECK_SAMPLES / NA
Instead of producing the normal comparison of read-groups, roll fingerprints up to the sample level and print out a sample x sample matrix with LOD scores.
boolean false
--EXIT_CODE_WHEN_MISMATCH / NA
When one or more mismatches between groups is detected, exit with this value instead of 0.
int 1 [ [ -∞ ∞ ] ]
--EXPECT_ALL_GROUPS_TO_MATCH / NA
Expect all groups' fingerprints to match, irrespective of their sample names. By default (with this value set to false), groups (readgroups, libraries, files, or samples) with different sample names are expected to mismatch, and those with the same sample name are expected to match.
boolean false
--EXPECT_ALL_READ_GROUPS_TO_MATCH / NA
Expect all read groups' fingerprints to match, irrespective of their sample names. By default (with this value set to false), read groups with different sample names are expected to mismatch, and those with the same sample name are expected to match.
Exclusion: This argument cannot be used at the same time as EXPECT_ALL_GROUPS_TO_MATCH
.
boolean false
--GA4GH_CLIENT_SECRETS / NA
Google Genomics API client_secrets.json file path.
String client_secrets.json
--GENOTYPING_ERROR_RATE / NA
Assumed genotyping error rate that provides a floor on the probability that a genotype comes from the expected sample. Must be greater than zero.
double 0.01 [ [ -∞ ∞ ] ]
--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 (or lists of files) with which to compare fingerprints.
R List[String] []
--INPUT_SAMPLE_MAP / NA
A tsv with two columns representing the sample as it appears in the INPUT data (in column 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT.
File null
--LOD_THRESHOLD / -LOD
If any two groups (with the same sample name) match with a LOD score lower than the threshold the tool will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD.
LOD score 0 means equal likelihood that the groups match vs. come from different individuals, negative LOD score -N, mean 10^N time more likely that the groups are from different individuals, and +N means 10^N times more likely that the groups are from the same individual.
double 0.0 [ [ -∞ ∞ ] ]
--LOSS_OF_HET_RATE / NA
The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via loss of heterozygosity) in the tumor (model assumes independent events, so this needs to be larger than reality).
double 0.5 [ [ -∞ ∞ ] ]
--MATRIX_OUTPUT / -MO
Optional output file to write matrix of LOD scores to. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Heterozygosity). It is however sometimes easier to use visually.
Exclusion: This argument cannot be used at the same time as SECOND_INPUT
.
File null
--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 [ [ -∞ ∞ ] ]
--NUM_THREADS / NA
The number of threads to use to process files and generate fingerprints.
int 1 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Optional output file to write metrics to. Default is to write to stdout.
File null
--OUTPUT_ERRORS_ONLY / NA
If true then only groups that do not relate to each other as expected will have their LODs reported.
boolean false
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--SECOND_INPUT / -SI
A second set of input files (or lists of files) with which to compare fingerprints. If this option is provided the tool compares each sample in INPUT with the sample from SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool will proceed to check the matching samples, but report the missing samples and return a non-zero error-code.
Exclusion: This argument cannot be used at the same time as MATRIX_OUTPUT, MO
.
List[String] []
--SECOND_INPUT_SAMPLE_MAP / NA
A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in column 1) and the sample as it should be used for comparisons to INPUT (in the second column). Need only include the samples that change. Values in column 1 should be unique. Values in column 2 should be unique even in union with the remaining unmapped samples. Should only be used with SECOND_INPUT.
File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR / NA
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 / NA
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 / NA
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 / NA
display the version number for this tool
boolean false
GATK version 4.0.12.0 built at 23-45-2019 03:45:45.
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