Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.
This tool uses reduced representation bisulfite sequencing (Rrbs) data to determine cytosine methylation status across all reads of a genomic DNA sequence. For a primer on bisulfite sequencing and cytosine methylation, please see the corresponding GATK Dictionary entry.
Briefly, bisulfite reduction converts un-methylated cytosine (C) to uracil (U) bases. Methylated sites are not converted because they are resistant to bisulfite reduction. Subsequent to PCR amplification of the reaction products, bisulfite reduction manifests as [C -> T (+ strand) or G -> A (- strand)] base conversions. Thus, conversion rates can be calculated from the reads as follows: [CR = converted/(converted + unconverted)]. Since methylated cytosines are protected against Rrbs-mediated conversion, the methylation rate (MR) is as follows:[MR = unconverted/(converted + unconverted) = (1 - CR)].
The CpG CollectRrbsMetrics tool outputs three files including summary and detail metrics tables as well as a PDF file containing four graphs. These graphs are derived from the summary table and include a comparison of conversion rates for both CpG and non-CpG sites, the distribution of total numbers of CpG sites as a function of the CpG conversion rates, the distribution of CpG sites by the level of read coverage (depth), and the numbers of reads discarded resulting from either exceeding the mismatch rate or size (too short). The detailed metrics table includes the coordinates of all of the CpG sites for the experiment as well as the conversion rates observed for each site.
java -jar picard.jar CollectRrbsMetrics \
Please see the CollectRrbsMetrics definitions for a complete description of both the detail and summary metrics produced by this tool.
Category Diagnostics and Quality Control
OverviewCalculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
CollectRrbsMetrics (Picard) specific arguments
|Argument name(s)||Default value||Summary|
|null||The BAM or SAM file containing aligned reads. Must be coordinate sorted|
|null||Base name for output files|
|null||The reference sequence fasta file|
|Optional Tool Arguments|
||||read one or more arguments files and add them to the command line|
|false||If true, assume that the input file is coordinate sorted even if the header says otherwise.|
||20||Threshold for base quality of a C base before it is considered|
|false||display the help message|
||0.1||Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1|
|[ALL_READS]||The level(s) at which to accumulate metrics.|
||5||Minimum read length|
||10||Threshold for quality of a base next to a C before the C base is considered|
||||Set of sequence names to consider, if not specified all sequences will be used|
||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.|
||||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_file / NA
read one or more arguments files and add them to the command line
--ASSUME_SORTED / -AS
If true, assume that the input file is coordinate sorted even if the header says otherwise.
Threshold for base quality of a C base before it is considered
int 20 [ [ -∞ ∞ ] ]
--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.
Google Genomics API client_secrets.json file path.
--help / -h
display the help message
--INPUT / -I
The BAM or SAM file containing aligned reads. Must be coordinate sorted
R File null
--MAX_MISMATCH_RATE / NA
Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1
double 0.1 [ [ -∞ ∞ ] ]
--MAX_RECORDS_IN_RAM / NA
Integer 500000 [ [ -∞ ∞ ] ]
--METRIC_ACCUMULATION_LEVEL / -LEVEL
The level(s) at which to accumulate metrics.
Base name for output files
R String null
Minimum read length
int 5 [ [ -∞ ∞ ] ]
Threshold for quality of a base next to a C before the C base is considered
int 10 [ [ -∞ ∞ ] ]
--QUIET / NA
Whether to suppress job-summary info on System.err.
--REFERENCE / -R
The reference sequence fasta file
R File null
--SEQUENCE_NAMES / NA
Set of sequence names to consider, if not specified all sequences will be used
--showHidden / -showHidden
display hidden arguments
--TMP_DIR / NA
--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
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
--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.