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**EXPERIMENTAL** CollectWgsMetricsWithNonZeroCoverage (Picard)

Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. This tool collects metrics about the percentages of reads that pass base- and mapping- quality filters as well as coverage (read-depth) levels. Both minimum base- and mapping-quality values as well as the maximum read depths (coverage cap) are user defined. This extends CollectWgsMetrics by including metrics related only to siteswith non-zero (>0) coverage.

Note: Metrics labeled as percentages are actually expressed as fractions!

Usage Example:

java -jar picard.jar CollectWgsMetricsWithNonZeroCoverage \
I=input.bam \
O=collect_wgs_metrics.txt \
CHART=collect_wgs_metrics.pdf \
R=reference_sequence.fasta
Please see the WgsMetricsWithNonZeroCoverage documentation for detailed explanations of the output metrics.

Category Diagnostics and Quality Control


Overview

CollectWgsMetricsWithNonZeroCoverage (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
--CHART_OUTPUT
 -CHART
null A file (with .pdf extension) to write the chart to.
--INPUT
 -I
null Input SAM or BAM file.
--OUTPUT
 -O
null Output metrics file.
--REFERENCE_SEQUENCE
 -R
null Reference sequence file.
Optional Tool Arguments
--ALLELE_FRACTION
[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] Allele fraction for which to calculate theoretical sensitivity.
--arguments_file
[] read one or more arguments files and add them to the command line
--COUNT_UNPAIRED
false If true, count unpaired reads, and paired reads with one end unmapped
--COVERAGE_CAP
 -CAP
250 Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).
--help
 -h
false display the help message
--INCLUDE_BQ_HISTOGRAM
false Determines whether to include the base quality histogram in the metrics file.
--INTERVALS
null An interval list file that contains the positions to restrict the assessment. Please note that all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs.
--LOCUS_ACCUMULATION_CAP
100000 At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low
--MINIMUM_BASE_QUALITY
 -Q
20 Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter.
--MINIMUM_MAPPING_QUALITY
 -MQ
20 Minimum mapping quality for a read to contribute coverage.
--READ_LENGTH
150 Average read length in the file. Default is 150.
--SAMPLE_SIZE
10000 Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.
--STOP_AFTER
-1 For debugging purposes, stop after processing this many genomic bases.
--THEORETICAL_SENSITIVITY_OUTPUT
null Output for Theoretical Sensitivity metrics.
--USE_FAST_ALGORITHM
false If true, fast algorithm is used.
--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.
--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.


--ALLELE_FRACTION / NA

Allele fraction for which to calculate theoretical sensitivity.

List[Double]  [0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]


--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []


--CHART_OUTPUT / -CHART

A file (with .pdf extension) to write the chart to.

R File  null


--COMPRESSION_LEVEL / NA

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]


--COUNT_UNPAIRED / NA

If true, count unpaired reads, and paired reads with one end unmapped

boolean  false


--COVERAGE_CAP / -CAP

Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).

int  250  [ [ -∞  ∞ ] ]


--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


--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json


--help / -h

display the help message

boolean  false


--INCLUDE_BQ_HISTOGRAM / NA

Determines whether to include the base quality histogram in the metrics file.

boolean  false


--INPUT / -I

Input SAM or BAM file.

R File  null


--INTERVALS / NA

An interval list file that contains the positions to restrict the assessment. Please note that all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs.

File  null


--LOCUS_ACCUMULATION_CAP / NA

At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low

int  100000  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--MINIMUM_BASE_QUALITY / -Q

Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter.

int  20  [ [ -∞  ∞ ] ]


--MINIMUM_MAPPING_QUALITY / -MQ

Minimum mapping quality for a read to contribute coverage.

int  20  [ [ -∞  ∞ ] ]


--OUTPUT / -O

Output metrics file.

R File  null


--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false


--READ_LENGTH / NA

Average read length in the file. Default is 150.

int  150  [ [ -∞  ∞ ] ]


--REFERENCE_SEQUENCE / -R

Reference sequence file.

R File  null


--SAMPLE_SIZE / NA

Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.

int  10000  [ [ -∞  ∞ ] ]


--showHidden / -showHidden

display hidden arguments

boolean  false


--STOP_AFTER / NA

For debugging purposes, stop after processing this many genomic bases.

long  -1  [ [ -∞  ∞ ] ]


--THEORETICAL_SENSITIVITY_OUTPUT / NA

Output for Theoretical Sensitivity metrics.

File  null


--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_FAST_ALGORITHM / NA

If true, fast algorithm is used.

boolean  false


--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


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GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.