Apply tranche filtering
Category Variant Filtering
Overview
Apply tranche filtering to VCF based on scores from an annotation in the INFO field. The annotation can come from the CNNScoreVariants tool (CNNLOD), VQSR (VQSLOD), or any other variant scoring tool which adds numeric annotations in a VCF's INFO field. Tranches are specified in percent sensitivity to the variants in the resource files. For example, if you specify INDEL tranches 98.0 and 99.0 using the CNN_2D score the filtered VCF will contain 2 filter tranches for INDELS: CNN_2D_INDEL_Tranche_98.00_99.00 and CNN_2D_INDEL_Tranche_99.00_100.00. Variants that scored better than the 98th percentile of variants in the resources pass through the filter and will have `PASS` in the filter field. We expect variants in the tranche CNN_2D_INDEL_Tranche_99.00_100.00 to be more sensitive, but less precise than CNN_2D_INDEL_Tranche_98.00_99.00, because variants in CNN_2D_INDEL_Tranche_99.00_100.00 have lower scores than variants in the tranche CNN_2D_INDEL_Tranche_98.00_99.00. The default tranche filtering threshold for SNPs is 99.95 and for INDELs it is 99.4. These thresholds maximize the F1 score (the harmonic mean of sensitivity and precision) for whole genome human data but may need to be tweaked for different datasets.Inputs
- The input variants to tranche filter.
- resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
- info-key The key from the INFO field of the VCF which contains the values that will be used to filter.
- tranche List of percent sensitivities to the known sites at which we will filter. Must be between 0 and 100.
Outputs
- A tranche filtered VCF.
Usage example
Apply tranche filters based on the scores in the info field with key CNN_1D.
gatk FilterVariantTranches \ -V input.vcf.gz \ --resource hapmap.vcf \ --resource mills.vcf \ --info-key CNN_1D \ --snp-tranche 99.95 \ --indel-tranche 99.4 \ -O filtered.vcf
Apply tranche filters based on the scores in the info field with key CNN_2D and remove any existing filters from the VCF.
gatk FilterVariantTranches \ -V input.vcf.gz \ --resource hapmap.vcf \ --resource mills.vcf \ --info-key CNN_2D \ --snp-tranche 99.95 \ --indel-tranche 99.4 \ --invalidate-previous-filters \ -O filtered.vcf
Apply several tranche filters based on the scores in the info field with key CNN_2D.
This will result in a VCF with filters: CNN_2D_SNP_Tranche_99.90_99.95, CNN_2D_SNP_Tranche_99.95_100.00 CNN_2D_INDEL_Tranche_99.00_99.50, CNN_2D_INDEL_Tranche_99.50_100.00. The interpretation is that `PASS` variants are the best, variants in the tranche `CNN_2D_INDEL_Tranche_99.00_99.50` are ok and variants in the tranche `CNN_2D_INDEL_Tranche_99.50_100.00` are the worst.gatk FilterVariantTranches \ -V input.vcf.gz \ --resource hapmap.vcf \ --resource mills.vcf \ --info-key CNN_2D \ --snp-tranche 99.9 --snp-tranche 99.95 \ --indel-tranche 99.0 --indel-tranche 99.4 \ -O filtered.vcf
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by FilterVariantTranches.
FilterVariantTranches 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 | |||
--output -O |
Output VCF file | ||
--resource |
A list of validated VCFs with known sites of common variation | ||
--variant -V |
A VCF file containing variants | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--cloud-index-prefetch-buffer -CIPB |
-1 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset. | |
--cloud-prefetch-buffer -CPB |
40 | Size of the cloud-only prefetch buffer (in MB; 0 to disable). | |
--disable-bam-index-caching -DBIC |
false | If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified. | |
--disable-sequence-dictionary-validation |
false | If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk! | |
--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 | |
--indel-tranche |
[99.4] | The level(s) of sensitivity to indels in the resource VCFs at which to filter indels. Higher numbers mean more desired sensitivity and thus less stringent filtering.Specified in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent. | |
--info-key |
CNN_2D | The key must be in the INFO field of the input VCF. | |
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
One or more genomic intervals over which to operate | ||
--invalidate-previous-filters |
false | Remove all filters that already exist in the VCF. | |
--reference -R |
Reference sequence | ||
--sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
--snp-tranche |
[99.95] | The level(s) of sensitivity to SNPs in the resource VCFs at which to filter SNPs. Higher numbers mean more desired sensitivity and thus less stringent filtering.Specified in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent. | |
--version |
false | display the version number for this tool | |
Optional Common Arguments | |||
--add-output-sam-program-record |
true | If true, adds a PG tag to created SAM/BAM/CRAM files. | |
--add-output-vcf-command-line |
true | If true, adds a command line header line to created VCF files. | |
--create-output-bam-index -OBI |
true | If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. | |
--create-output-bam-md5 -OBM |
false | If true, create a MD5 digest for any BAM/SAM/CRAM file created | |
--create-output-variant-index -OVI |
true | If true, create a VCF index when writing a coordinate-sorted VCF file. | |
--create-output-variant-md5 -OVM |
false | If true, create a a MD5 digest any VCF file created. | |
--disable-read-filter -DF |
Read filters to be disabled before analysis | ||
--disable-tool-default-read-filters |
false | Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on) | |
--exclude-intervals -XL |
One or more genomic intervals to exclude from processing | ||
--gatk-config-file |
A configuration file to use with the GATK. | ||
--input -I |
BAM/SAM/CRAM file containing reads | ||
--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 | |
--lenient -LE |
false | Lenient processing of VCF files | |
--max-variants-per-shard |
0 | If non-zero, partitions VCF output into shards, each containing up to the given number of records. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--read-filter -RF |
Read filters to be applied before analysis | ||
--read-index |
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically. | ||
--read-validation-stringency -VS |
SILENT | Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
--seconds-between-progress-updates |
10.0 | Output traversal statistics every time this many seconds elapse | |
--sequence-dictionary |
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file. | ||
--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.
--add-output-sam-program-record / -add-output-sam-program-record
If true, adds a PG tag to created SAM/BAM/CRAM files.
boolean true
--add-output-vcf-command-line / -add-output-vcf-command-line
If true, adds a command line header line to created VCF files.
boolean true
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--cloud-index-prefetch-buffer / -CIPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.
int -1 [ [ -∞ ∞ ] ]
--cloud-prefetch-buffer / -CPB
Size of the cloud-only prefetch buffer (in MB; 0 to disable).
int 40 [ [ -∞ ∞ ] ]
--create-output-bam-index / -OBI
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.
boolean true
--create-output-bam-md5 / -OBM
If true, create a MD5 digest for any BAM/SAM/CRAM file created
boolean false
--create-output-variant-index / -OVI
If true, create a VCF index when writing a coordinate-sorted VCF file.
boolean true
--create-output-variant-md5 / -OVM
If true, create a a MD5 digest any VCF file created.
boolean false
--disable-bam-index-caching / -DBIC
If true, don't cache bam indexes, this will reduce memory requirements but may harm performance if many intervals are specified. Caching is automatically disabled if there are no intervals specified.
boolean false
--disable-read-filter / -DF
Read filters to be disabled before analysis
List[String] []
--disable-sequence-dictionary-validation / -disable-sequence-dictionary-validation
If specified, do not check the sequence dictionaries from our inputs for compatibility. Use at your own risk!
boolean false
--disable-tool-default-read-filters / -disable-tool-default-read-filters
Disable all tool default read filters (WARNING: many tools will not function correctly without their default read filters on)
boolean false
--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] []
--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
--indel-tranche / -indel-tranche
The level(s) of sensitivity to indels in the resource VCFs at which to filter indels. Higher numbers mean more desired sensitivity and thus less stringent filtering.Specified in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent.
List[Double] [99.4]
--info-key / -info-key
The key must be in the INFO field of the input VCF.
String CNN_2D
--input / -I
BAM/SAM/CRAM file containing reads
List[GATKPath] []
--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
List[String] []
--invalidate-previous-filters
Remove all filters that already exist in the VCF.
boolean false
--lenient / -LE
Lenient processing of VCF files
boolean false
--max-variants-per-shard
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
--output / -O
Output VCF file
R GATKPath null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--read-filter / -RF
Read filters to be applied before analysis
List[String] []
--read-index / -read-index
Indices to use for the read inputs. If specified, an index must be provided for every read input and in the same order as the read inputs. If this argument is not specified, the path to the index for each input will be inferred automatically.
List[GATKPath] []
--read-validation-stringency / -VS
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value 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 --read-validation-stringency argument is an enumerated type (ValidationStringency), which can have one of the following values:
- STRICT
- LENIENT
- SILENT
ValidationStringency SILENT
--reference / -R
Reference sequence
GATKPath null
--resource
A list of validated VCFs with known sites of common variation
R List[FeatureInput[VariantContext]] []
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--sequence-dictionary / -sequence-dictionary
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
GATKPath null
--showHidden / -showHidden
display hidden arguments
boolean false
--sites-only-vcf-output
If true, don't emit genotype fields when writing vcf file output.
boolean false
--snp-tranche / -snp-tranche
The level(s) of sensitivity to SNPs in the resource VCFs at which to filter SNPs. Higher numbers mean more desired sensitivity and thus less stringent filtering.Specified in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent.
List[Double] [99.95]
--tmp-dir
Temp directory to use.
GATKPath 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
--variant / -V
A VCF file containing variants
R GATKPath null
--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
display the version number for this tool
boolean false
GATK version 4.2.6.1-SNAPSHOT built at Wed, 13 Apr 2022 13:12:10 -0700.
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