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**EXPERIMENTAL** FilterAlignmentArtifacts

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 bam input to this tool should be the reassembly bamout produced by HaplotypeCaller or Mutect2 in the process of generating the input callset. The original bam will also work but might fail to filter some indels. The reference passed with the -R argument must be the reference to which the input bam was realigned. 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.

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
null BWA-mem index image
--input
 -I
[] BAM/SAM/CRAM file containing reads
--output
 -O
null The output filtered VCF file
--variant
 -V
null 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!
--dont-skip-filtered-variants
false Try to realign all variants, even ones that have already been filtered.
--dont-use-mates
false Realign individual reads without using their mates
--drop-ratio
0.2 Fraction of best MEM extension score below which other extensions are dropped
--fragment-size
1000 Distance away from variant to look for reads' mates.
--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
--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
--max-failed-realignments
3 Maximum number of failed read realignments before a variant is rejected.
--max-reasonable-fragment-length
100000 Maximum fragment length to be considered a reasonable pair alignment
--min-aligner-score-difference
20 Minimum difference between best and second-best alignment for a read to be considered well-mapped
--min-mismatch-ratio
2.5 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
25 Number of regular i.e. non-alt contigs
--reference
 -R
null Reference sequence
--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.
--sufficient-good-realignments
2 Sufficient number of good read realignments to accept a variant.
--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
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
--lenient
 -LE
false Lenient processing of VCF files
--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
null Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.
--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.


--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 / NA

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

List[File]  []


--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  [ [ -∞  ∞ ] ]


--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 / NA

Try to realign all variants, even ones that have already been filtered.

boolean  false


--dont-use-mates / NA

Realign individual reads without using their mates
Turn off the default mate-aware realignment

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]  []


--fragment-size / NA

Distance away from variant to look for reads' mates.

int  1000  [ [ -∞  ∞ ] ]


--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


--indel-start-tolerance / NA

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[String]  []


--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]  []


--lenient / -LE

Lenient processing of VCF files

boolean  false


--max-failed-realignments / NA

Maximum number of failed read realignments before a variant is rejected.

int  3  [ [ -∞  ∞ ] ]


--max-reasonable-fragment-length / NA

Maximum fragment length to be considered a reasonable pair alignment
Maximum fragment length to be considered a reasonable pair alignment

int  100000  [ [ -∞  ∞ ] ]


--min-aligner-score-difference / NA

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

int  20  [ [ -∞  ∞ ] ]


--min-mismatch-ratio / NA

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  2.5  [ [ -∞  ∞ ] ]


--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 / NA

Number of regular i.e. non-alt contigs
Number of regular i.e. non-alt contigs

int  25  [ [ -∞  ∞ ] ]


--output / -O

The output filtered VCF file

R String  null


--QUIET / NA

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[String]  []


--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

String  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.

String  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--sites-only-vcf-output / NA

If true, don't emit genotype fields when writing vcf file output.

boolean  false


--sufficient-good-realignments / NA

Sufficient number of good read realignments to accept a variant.

int  2  [ [ -∞  ∞ ] ]


--tmp-dir / NA

Temp directory to use.

String  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 String  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 / 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.