Filters intervals based on annotations and/or count statistics
Category Copy Number Variant Discovery
Overview
Given specified intervals, annotated intervals output by AnnotateIntervals, and/or counts output by CollectReadCounts, outputs a filtered Picard interval list. The set intersection of intervals from the specified intervals, the annotated intervals, and the first count file will be taken as the initial set of intervals on which to perform filtering. Parameters for filtering based on the annotations and counts can be adjusted. Annotation-based filters will be applied first, followed by count-based filters. The result may be passed via -L to other tools (e.g., DetermineGermlineContigPloidy and GermlineCNVCaller) to mask intervals from analysis.Inputs
- Intervals to be filtered (typically, the bins output by PreprocessIntervals). The argument interval-merging-rule must be set to IntervalMergingRule#OVERLAPPING_ONLY and all other common arguments for interval padding or merging must be set to their defaults. A blacklist of regions in which intervals should always be filtered (regardless of other annotation-based or count-based filters) may also be provided via -XL; this can be used to filter pseudoautosomal regions (PARs), for example. Partial bins created by interval exclusion may be dropped upon intersection with the intervals present in other optional inputs.
- (Optional) Annotated-intervals file from AnnotateIntervals. Must be provided if no counts files are provided.
- (Optional) Counts files (TSV or HDF5 output of CollectReadCounts). Must be provided if no annotated-intervals file is provided.
Output
- Filtered Picard interval-list file.
Usage examples
gatk FilterIntervals \
-L preprocessed_intervals.interval_list \
-XL blacklist_intervals.interval_list \
-I sample_1.counts.hdf5 \
-I sample_2.counts.hdf5 \
... \
--annotated-intervals annotated_intervals.tsv \
-O filtered_intervals.interval_list
gatk FilterIntervals \
-L preprocessed_intervals.interval_list \
--annotated-intervals annotated_intervals.tsv \
-O filtered_intervals.interval_list
gatk FilterIntervals \
-L preprocessed_intervals.interval_list \
-I sample_1.counts.hdf5 \
-I sample_2.counts.hdf5 \
... \
-O filtered_intervals.interval_list
FilterIntervals 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 | |||
| --intervals -L |
[] | One or more genomic intervals over which to operate | |
| --output -O |
null | Output Picard interval-list file containing the filtered intervals. | |
| Optional Tool Arguments | |||
| --annotated-intervals |
null | Input file containing annotations for genomic intervals (output of AnnotateIntervals). Must be provided if no counts files are provided. | |
| --arguments_file |
[] | read one or more arguments files and add them to the command line | |
| --extreme-count-filter-maximum-percentile |
99.0 | Maximum-percentile parameter for the extreme-count filter. Intervals with a count that has a percentile strictly greater than this in a percentage of samples strictly greater than extreme-count-filter-percentage-of-samples will be filtered out. (This is the second count-based filter applied.) | |
| --extreme-count-filter-minimum-percentile |
1.0 | Minimum-percentile parameter for the extreme-count filter. Intervals with a count that has a percentile strictly less than this in a percentage of samples strictly greater than extreme-count-filter-percentage-of-samples will be filtered out. (This is the second count-based filter applied.) | |
| --extreme-count-filter-percentage-of-samples |
90.0 | Percentage-of-samples parameter for the extreme-count filter. Intervals with a count that has a percentile outside of [extreme-count-filter-minimum-percentile, extreme-count-filter-maximum-percentile] in a percentage of samples strictly greater than this will be filtered out. (This is the second count-based filter applied.) | |
| --gcs-max-retries -gcs-retries |
20 | If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection | |
| --gcs-project-for-requester-pays |
"" | Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. | |
| --help -h |
false | display the help message | |
| --input -I |
[] | Input TSV or HDF5 files containing integer read counts in genomic intervals (output of CollectReadCounts). Must be provided if no annotated-intervals file is provided. | |
| --interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
| --low-count-filter-count-threshold |
5 | Count-threshold parameter for the low-count filter. Intervals with a count strictly less than this threshold in a percentage of samples strictly greater than low-count-filter-percentage-of-samples will be filtered out. (This is the first count-based filter applied.) | |
| --low-count-filter-percentage-of-samples |
90.0 | Percentage-of-samples parameter for the low-count filter. Intervals with a count strictly less than low-count-filter-count-threshold in a percentage of samples strictly greater than this will be filtered out. (This is the first count-based filter applied.) | |
| --maximum-gc-content |
0.9 | Maximum allowed value for GC-content annotation (inclusive). | |
| --maximum-mappability |
1.0 | Maximum allowed value for mappability annotation (inclusive). | |
| --maximum-segmental-duplication-content |
0.5 | Maximum allowed value for segmental-duplication-content annotation (inclusive). | |
| --minimum-gc-content |
0.1 | Minimum allowed value for GC-content annotation (inclusive). | |
| --minimum-mappability |
0.9 | Minimum allowed value for mappability annotation (inclusive). | |
| --minimum-segmental-duplication-content |
0.0 | Minimum allowed value for segmental-duplication-content annotation (inclusive). | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --exclude-intervals -XL |
[] | One or more genomic intervals to exclude from processing | |
| --gatk-config-file |
null | A configuration file to use with the GATK. | |
| --interval-exclusion-padding -ixp |
0 | Amount of padding (in bp) to add to each interval you are excluding. | |
| --interval-padding -ip |
0 | Amount of padding (in bp) to add to each interval you are including. | |
| --interval-set-rule -isr |
UNION | Set merging approach to use for combining interval inputs | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --tmp-dir |
null | Temp directory to use. | |
| --use-jdk-deflater -jdk-deflater |
false | Whether to use the JdkDeflater (as opposed to IntelDeflater) | |
| --use-jdk-inflater -jdk-inflater |
false | Whether to use the JdkInflater (as opposed to IntelInflater) | |
| --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.
--annotated-intervals / NA
Input file containing annotations for genomic intervals (output of AnnotateIntervals). Must be provided if no counts files are provided.
File null
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--exclude-intervals / -XL
One or more genomic intervals to exclude from processing
Use this argument to exclude certain parts of the genome from the analysis (like -L, but the opposite).
This argument can be specified multiple times. You can use samtools-style intervals either explicitly on the
command line (e.g. -XL 1 or -XL 1:100-200) or by loading in a file containing a list of intervals
(e.g. -XL myFile.intervals).
List[String] []
--extreme-count-filter-maximum-percentile / NA
Maximum-percentile parameter for the extreme-count filter. Intervals with a count that has a percentile strictly greater than this in a percentage of samples strictly greater than extreme-count-filter-percentage-of-samples will be filtered out. (This is the second count-based filter applied.)
double 99.0 [ [ 0 100 ] ]
--extreme-count-filter-minimum-percentile / NA
Minimum-percentile parameter for the extreme-count filter. Intervals with a count that has a percentile strictly less than this in a percentage of samples strictly greater than extreme-count-filter-percentage-of-samples will be filtered out. (This is the second count-based filter applied.)
double 1.0 [ [ 0 100 ] ]
--extreme-count-filter-percentage-of-samples / NA
Percentage-of-samples parameter for the extreme-count filter. Intervals with a count that has a percentile outside of [extreme-count-filter-minimum-percentile, extreme-count-filter-maximum-percentile] in a percentage of samples strictly greater than this will be filtered out. (This is the second count-based filter applied.)
double 90.0 [ [ 0 100 ] ]
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--gcs-max-retries / -gcs-retries
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
--gcs-project-for-requester-pays / NA
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
String ""
--help / -h
display the help message
boolean false
--input / -I
Input TSV or HDF5 files containing integer read counts in genomic intervals (output of CollectReadCounts). Must be provided if no annotated-intervals file is provided.
List[File] []
--interval-exclusion-padding / -ixp
Amount of padding (in bp) to add to each interval you are excluding.
Use this to add padding to the intervals specified using -XL. For example, '-XL 1:100' with a
padding value of 20 would turn into '-XL 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-merging-rule / -imr
Interval merging rule for abutting intervals
By default, the program merges abutting intervals (i.e. intervals that are directly side-by-side but do not
actually overlap) into a single continuous interval. However you can change this behavior if you want them to be
treated as separate intervals instead.
The --interval-merging-rule argument is an enumerated type (IntervalMergingRule), which can have one of the following values:
- ALL
- OVERLAPPING_ONLY
IntervalMergingRule ALL
--interval-padding / -ip
Amount of padding (in bp) to add to each interval you are including.
Use this to add padding to the intervals specified using -L. For example, '-L 1:100' with a
padding value of 20 would turn into '-L 1:80-120'. This is typically used to add padding around targets when
analyzing exomes.
int 0 [ [ -∞ ∞ ] ]
--interval-set-rule / -isr
Set merging approach to use for combining interval inputs
By default, the program will take the UNION of all intervals specified using -L and/or -XL. However, you can
change this setting for -L, for example if you want to take the INTERSECTION of the sets instead. E.g. to
perform the analysis only on chromosome 1 exomes, you could specify -L exomes.intervals -L 1 --interval-set-rule
INTERSECTION. However, it is not possible to modify the merging approach for intervals passed using -XL (they will
always be merged using UNION).
Note that if you specify both -L and -XL, the -XL interval set will be subtracted from the -L interval set.
The --interval-set-rule argument is an enumerated type (IntervalSetRule), which can have one of the following values:
- UNION
- Take the union of all intervals
- INTERSECTION
- Take the intersection of intervals (the subset that overlaps all intervals specified)
IntervalSetRule UNION
--intervals / -L
One or more genomic intervals over which to operate
R List[String] []
--low-count-filter-count-threshold / NA
Count-threshold parameter for the low-count filter. Intervals with a count strictly less than this threshold in a percentage of samples strictly greater than low-count-filter-percentage-of-samples will be filtered out. (This is the first count-based filter applied.)
int 5 [ [ 0 ∞ ] ]
--low-count-filter-percentage-of-samples / NA
Percentage-of-samples parameter for the low-count filter. Intervals with a count strictly less than low-count-filter-count-threshold in a percentage of samples strictly greater than this will be filtered out. (This is the first count-based filter applied.)
double 90.0 [ [ 0 100 ] ]
--maximum-gc-content / NA
Maximum allowed value for GC-content annotation (inclusive).
double 0.9 [ [ 0 1 ] ]
--maximum-mappability / NA
Maximum allowed value for mappability annotation (inclusive).
double 1.0 [ [ 0 1 ] ]
--maximum-segmental-duplication-content / NA
Maximum allowed value for segmental-duplication-content annotation (inclusive).
double 0.5 [ [ 0 1 ] ]
--minimum-gc-content / NA
Minimum allowed value for GC-content annotation (inclusive).
double 0.1 [ [ 0 1 ] ]
--minimum-mappability / NA
Minimum allowed value for mappability annotation (inclusive).
double 0.9 [ [ 0 1 ] ]
--minimum-segmental-duplication-content / NA
Minimum allowed value for segmental-duplication-content annotation (inclusive).
double 0.0 [ [ 0 1 ] ]
--output / -O
Output Picard interval-list file containing the filtered intervals.
R File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--tmp-dir / NA
Temp directory to use.
GATKPathSpecifier null
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--verbosity / -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 / NA
display the version number for this tool
boolean false
GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.
0 comments
Please sign in to leave a comment.