Produces a summary of alignment metrics from a SAM or BAM file. This tool takes a SAM/BAM file input and produces metrics detailing the quality of the read alignments as well as the proportion of the reads that passed machine signal-to-noise threshold quality filters. Note that these quality filters are specific to Illumina data; for additional information, please see the corresponding GATK Dictionary entry.
Note: Metrics labeled as percentages are actually expressed as fractions!
java -jar picard.jar CollectAlignmentSummaryMetrics \
Please see the CollectAlignmentSummaryMetrics definitions for a complete description of the metrics produced by this tool.
Category Diagnostics and Quality Control
OverviewA command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment. Metrics to include, but not limited to:
- Total number of reads (total, period, no exclusions)
- Total number of PF reads (PF == does not fail vendor check flag)
- Number of PF noise reads (does not fail vendor check and has noise attr set)
- Total aligned PF reads (any PF read that has a sequence and position)
- High quality aligned PF reads (high quality == mapping quality >= 20)
- High quality aligned PF bases (actual aligned bases, calculate off alignment blocks)
- High quality aligned PF Q20 bases (subset of above where base quality >= 20)
- Median mismatches in HQ aligned PF reads (how many aligned bases != ref on average)
- Reads aligned in pairs (vs. reads aligned with mate unaligned/not present)
- Read length (how to handle mixed lengths?)
- Bad Cycles - how many machine cycles yielded combined no-call and mismatch rates of >= 80%
- Strand balance - reads mapped to positive strand / total mapped reads
- the insert size is larger than MAX_INSERT_SIZE
- the ends of a pair map to different contigs
- the paired end orientation is different that the expected orientation
- the read contains an SA tag (chimeric alignment)
CollectAlignmentSummaryMetrics (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 SAM or BAM file.|
|null||File to write the output to.|
|Optional Tool Arguments|
||[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG]||List of adapter sequences to use when processing the alignment metrics.|
||||read one or more arguments files and add them to the command line|
|true||If true (default), then the sort order in the header file will be ignored.|
||[FR]||Paired-end reads that do not have this expected orientation will be considered chimeric.|
|false||display the help message|
|false||Whether the SAM or BAM file consists of bisulfite sequenced reads.|
||100000||Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs.|
|[ALL_READS]||The level(s) at which to accumulate metrics.|
|null||Reference sequence file. Note that while this argument isn't required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.|
||0||Stop after processing N reads, mainly for debugging.|
||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 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.
--ADAPTER_SEQUENCE / NA
List of adapter sequences to use when processing the alignment metrics.
List[String] [AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG]
--arguments_file / NA
read one or more arguments files and add them to the command line
--ASSUME_SORTED / -AS
If true (default), then the sort order in the header file will be ignored.
--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.
Paired-end reads that do not have this expected orientation will be considered chimeric.
Google Genomics API client_secrets.json file path.
--help / -h
display the help message
--INPUT / -I
Input SAM or BAM file.
R File null
--IS_BISULFITE_SEQUENCED / -BS
Whether the SAM or BAM file consists of bisulfite sequenced reads.
--MAX_INSERT_SIZE / NA
Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs.
int 100000 [ [ -∞ ∞ ] ]
--MAX_RECORDS_IN_RAM / NA
Integer 500000 [ [ -∞ ∞ ] ]
--METRIC_ACCUMULATION_LEVEL / -LEVEL
The level(s) at which to accumulate metrics.
--OUTPUT / -O
File to write the output to.
R File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
--REFERENCE_SEQUENCE / -R
Reference sequence file. Note that while this argument isn't required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary.
--showHidden / -showHidden
display hidden arguments
--STOP_AFTER / NA
Stop after processing N reads, mainly for debugging.
long 0 [ [ -∞ ∞ ] ]
--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 126.96.36.199 built at 02-47-2019 02:47:54.