FilterIntervals

Filters intervals based on annotations and/or count statistics

Category Copy Number Variant Discovery

Overview

Given specified intervals, annotated intervals output by {@link AnnotateIntervals}, and/or counts output by {@link 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. In the end, any singleton intervals (i.e., those being by themselves on their corresponding contigs) found after applying other filters will be filtered out. The result may be passed via -L to other tools (e.g., {@link DetermineGermlineContigPloidy} and {@link GermlineCNVCaller}) to mask intervals from analysis.

Inputs

Intervals to be filtered (typically, the bins output by {@link PreprocessIntervals}). The argument {@code interval-merging-rule} must be set to {@link 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 {@link AnnotateIntervals}. Must be provided if no counts files are provided.
(Optional) Counts files (TSV or HDF5 output of {@link CollectReadCounts}). Must be provided if no annotated-intervals file is provided.

Outputs

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

Caveats

Note that a minimum mappability greater than zero and/or a maximum segmental duplication content less than one both have the potential to exclude real variant calls by excluding their intervals due to these criteria.

@author Samuel Lee <slee@broadinstitute.org>

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		Output Picard interval-list file containing the filtered intervals.
Optional Tool Arguments
--annotated-intervals		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. User must have storage.buckets.get permission on the bucket being 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	10	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	50.0	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		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		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

Input file containing annotations for genomic intervals (output of AnnotateIntervals). Must be provided if no counts files are provided.

File null

--arguments_file

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). strings gathered from the command line -XL argument to be parsed into intervals to exclude

List[String] []

--extreme-count-filter-maximum-percentile

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

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

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

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

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being 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

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 10 [ [ 0 ∞ ] ]

--low-count-filter-percentage-of-samples

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 50.0 [ [ 0 100 ] ]