Filter alignment artifacts from a vcf callset.
Category Variant Filtering
Overview
Filter false positive alignment artifacts from a VCF callset.
FilterAlignmentArtifacts identifies alignment artifacts, that is, apparent variants due to reads being mapped to the wrong genomic locus.
Alignment artifacts can occur whenever there is sufficient sequence similarity between two or more regions in the genome to confuse the alignment algorithm. This can occur when the aligner for whatever reason overestimate how uniquely a read maps, thereby assigning it too high of a mapping quality. It can also occur through no fault of the aligner due to gaps in the reference, which can also hide the true position to which a read should map. By using a good alignment algorithm (the GATK wrapper of BWA-MEM), giving it sensitive settings (which may have been impractically slow for the original bam alignment) and mapping to the best available reference we can avoid these pitfalls. The last point is especially important: one can (and should) use a BWA-MEM index image corresponding to the best reference, regardless of the reference to which the bam was aligned.
This tool is featured in the Somatic Short Mutation calling Best Practice Workflow. See Tutorial#11136 for a step-by-step description of the workflow and Article#11127 for an overview of what traditional somatic calling entails. For the latest pipeline scripts, see the Mutect2 WDL scripts directory.
The input bam to this tool should be the same tumor bam that Mutect2 was run on. The reference passed with the -R argument must be the reference to which the input bam was aligned. This does not need to correspond to the reference of the BWA-MEM index image. The latter should be derived from the best available reference, for example hg38 in humans as of February 2018.
Usage example
gatk FilterAlignmentArtifacts \ -R hg19.fasta -V somatic.vcf.gz \ -I somatic_bamout.bam \ --bwa-mem-index-image hg38.index_image \ -O filtered.vcf.gz
Additional Information
Read filters
These Read Filters are automatically applied to the data by the Engine before processing by FilterAlignmentArtifacts.
- NonChimericOriginalAlignmentReadFilter
- NotSecondaryAlignmentReadFilter
- GoodCigarReadFilter
- NonZeroReferenceLengthAlignmentReadFilter
- PassesVendorQualityCheckReadFilter
- ReadLengthReadFilter
- MappedReadFilter
- MappingQualityAvailableReadFilter
- NotDuplicateReadFilter
- MappingQualityReadFilter
- MappingQualityNotZeroReadFilter
- WellformedReadFilter
FilterAlignmentArtifacts 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 | |||
--bwa-mem-index-image -index |
BWA-mem index image | ||
--input -I |
BAM/SAM/CRAM file containing reads | ||
--output -O |
The output filtered VCF file | ||
--reference -R |
Reference sequence file | ||
--variant -V |
One or more VCF files containing variants | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--bam-output -bamout |
File to which assembled haplotypes should be written | ||
--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! | |
--dont-skip-filtered-variants |
false | Try to realign all variants, even ones that have already been filtered. | |
--drop-ratio |
0.2 | Fraction of best MEM extension score below which other extensions are dropped | |
--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-start-tolerance |
5 | Max distance between indel start of aligned read in the bam and the variant in the vcf | |
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
One or more genomic intervals over which to operate | ||
--kmer-size |
21 | Kmer size for reassembly | |
--max-reasonable-fragment-length |
100000 | Maximum fragment length to be considered a reasonable pair alignment | |
--min-aligner-score-difference-per-base |
0.2 | Minimum difference between best and second-best alignment for a read to be considered well-mapped | |
--min-mismatch-difference-per-base |
0.02 | Minimum ratio between the number of mismatches in the second best and best alignments | |
--minimum-seed-length -min-seed-length |
14 | Minimum number of matching bases to seed a MEM | |
--num-regular-contigs |
250000 | Number of regular i.e. non-alt contigs | |
--seed-split-factor -split-factor |
0.5 | MEMs longer than the minimum seed length times this factor are split and re-seeded. | |
--sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
--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. | ||
--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 | |||
--combine-variants-distance |
1000 | Maximum distance for variants to be grouped together | |
--ignore-variants-starting-outside-interval |
false | Restrict variant output to sites that start within provided intervals (only applies when an interval is specified) | |
--max-distance |
10000 | Maximum distance for variants to be grouped together | |
--ref-padding |
100 | Number of bases on either side to expand spanning reference window | |
--showHidden |
false | display hidden arguments | |
--smith-waterman |
FASTEST_AVAILABLE | Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice |
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] []
--bam-output / -bamout
File to which assembled haplotypes should be written
String null
--bwa-mem-index-image / -index
BWA-mem index image
BWA-mem index image created by {@link BwaMemIndexImageCreator}
R String null
--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 [ [ -∞ ∞ ] ]
--combine-variants-distance
Maximum distance for variants to be grouped together
int 1000 [ [ -∞ ∞ ] ]
--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
--dont-skip-filtered-variants
Try to realign all variants, even ones that have already been filtered.
boolean false
--drop-ratio / -drop-ratio
Fraction of best MEM extension score below which other extensions are dropped
BWA-mem extension drop ratio
double 0.2 [ [ -∞ ∞ ] ]
--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
--ignore-variants-starting-outside-interval
Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)
this option has no effect unless intervals are specified.
This exists to mimic GATK3 interval traversal patterns
boolean false
--indel-start-tolerance
Max distance between indel start of aligned read in the bam and the variant in the vcf
int 5 [ [ -∞ ∞ ] ]
--input / -I
BAM/SAM/CRAM file containing reads
R 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] []
--kmer-size
Kmer size for reassembly
int 21 [ [ -∞ ∞ ] ]
--lenient / -LE
Lenient processing of VCF files
boolean false
--max-distance
Maximum distance for variants to be grouped together
int 10000 [ [ -∞ ∞ ] ]
--max-reasonable-fragment-length
Maximum fragment length to be considered a reasonable pair alignment
Maximum fragment length to be considered a reasonable pair alignment
int 100000 [ [ -∞ ∞ ] ]
--max-variants-per-shard
If non-zero, partitions VCF output into shards, each containing up to the given number of records.
int 0 [ [ 0 ∞ ] ]
--min-aligner-score-difference-per-base
Minimum difference between best and second-best alignment for a read to be considered well-mapped
Minimum difference between best and second-best alignment for a read to be considered well-mapped
double 0.2 [ [ -∞ ∞ ] ]
--min-mismatch-difference-per-base
Minimum ratio between the number of mismatches in the second best and best alignments
Minimum ratio between the number of mismatches in the second best and best alignments
double 0.02 [ [ -∞ ∞ ] ]
--minimum-seed-length / -min-seed-length
Minimum number of matching bases to seed a MEM
BWA-mem minimum seed length
int 14 [ [ -∞ ∞ ] ]
--num-regular-contigs
Number of regular i.e. non-alt contigs
Number of regular i.e. non-alt contigs
int 250000 [ [ -∞ ∞ ] ]
--output / -O
The output filtered 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
--ref-padding
Number of bases on either side to expand spanning reference window
int 100 [ [ -∞ ∞ ] ]
--reference / -R
Reference sequence file
R GATKPath null
--seconds-between-progress-updates / -seconds-between-progress-updates
Output traversal statistics every time this many seconds elapse
double 10.0 [ [ -∞ ∞ ] ]
--seed-split-factor / -split-factor
MEMs longer than the minimum seed length times this factor are split and re-seeded.
BWA-mem seed split factor
double 0.5 [ [ -∞ ∞ ] ]
--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
--smith-waterman
Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice
The --smith-waterman argument is an enumerated type (Implementation), which can have one of the following values:
- FASTEST_AVAILABLE
- use the fastest available Smith-Waterman aligner that runs on your hardware
- AVX_ENABLED
- use the AVX enabled Smith-Waterman aligner
- JAVA
- use the pure java implementation of Smith-Waterman, works on all hardware
Implementation FASTEST_AVAILABLE
--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
One or more VCF files containing variants
R List[GATKPath] []
--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 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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