Map/find features in BAM file, output VCF. Initially mapping SNVs
Category Flow Based Tools
Traversal ReadWalker
Overview
Finds specific features in reads, scores the confidence of each feature relative to the reference in each read and writes them into a VCF file. The sense of what a 'feature' is left somewhat open. In the most general sense, it is a haplotype located in a specific location on the read. It is not necessarily defined as a deviation from the reference. A feature is indeed scored against the reference (in terms of its deviation). The current version implements a single type of feature: a SNP (aka SNV).At this point, this tool finds SNVs
Input
- Coordinate-sorted and indexed SAM/BAM/CRAM
Output
- Coordinate-sorted and indexed VCF
Usage examples
Find SNVs in chromosome 20.gatk FlowFeatureMapper \ -I input.bam \ -L 20 \ -O chr20_snv.vcf{@GATK.walkertype ReadWalker}
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by FlowFeatureMapper.
FlowFeatureMapper 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 | |||
--input -I |
BAM/SAM/CRAM file containing reads | ||
--output -O |
File to which variants should be written | ||
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). | |
--copy-attr |
attributes to copy from bam | ||
--copy-attr-prefix |
prefix to add to attributes to copy from bam | ||
--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! | |
--exclude-nan-scores |
false | exclude nan scores | |
--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 | |
--include-dup-reads |
false | include duplicate reads | |
--interval-merging-rule -imr |
ALL | Interval merging rule for abutting intervals | |
--intervals -L |
One or more genomic intervals over which to operate | ||
--keep-negatives |
false | keep nevative scores? | |
--keep-supplementary-alignments |
false | keep supplementary alignments ? | |
--limit-score |
NaN | Limit value for score | |
--mapping-feature |
SNV | Kind of feaure being mapped | |
--max-score |
Infinity | threshold of score delta to for emitting (will be emitted if lower) | |
--min-score |
-Infinity | minimal threshold of score delta to for emitting (will be emitted if higher) | |
--reference -R |
Reference sequence | ||
--sites-only-vcf-output |
false | If true, don't emit genotype fields when writing vcf file output. | |
--snv-identical-bases |
1 | number of bases that need to be identical before the snv | |
--snv-identical-bases-after |
0 | number of bases that need to be identical after the snv. 0 means same as number of bases before | |
--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 | |||
--emit-ref-confidence -ERC |
NONE | Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature) | |
--floor-blocks |
false | Output the band lower bound for each GQ block regardless of the data it represents | |
--flow-disallow-probs-larger-than-call |
false | Cap probabilities of error to 1 relative to base call | |
--flow-fill-empty-bins-value |
0.001 | Value to fill the zeros of the matrix with | |
--flow-lump-probs |
false | Should all probabilities of insertion or deletion in the flow be combined together | |
--flow-matrix-mods |
Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12 | ||
--flow-probability-scaling-factor |
10 | probability scaling factor for (phred=10) for probability quantization | |
--flow-probability-threshold |
0.003 | Lowest probability ratio to be used as an option | |
--flow-quantization-bins |
121 | Number of bins for probability quantization | |
--flow-remove-non-single-base-pair-indels |
false | Should the probabilities of more then 1 indel be used | |
--flow-remove-one-zero-probs |
false | Remove probabilities of basecall of zero from non-zero genome | |
--flow-report-insertion-or-deletion |
false | Report either insertion or deletion, probability, not both | |
--flow-retain-max-n-probs-base-format |
false | Keep only hmer/2 probabilities (like in base format) | |
--flow-symmetric-indel-probs |
false | Should indel probabilities be symmetric in flow | |
--flow-use-t0-tag |
false | Use t0 tag if exists in the read to create flow matrix | |
--gvcf-gq-bands -GQB |
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] | Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order) | |
--keep-boundary-flows |
false | prevent spreading of boundary flows. | |
--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 [ [ -∞ ∞ ] ]
--copy-attr
attributes to copy from bam
attributes to copy from bam
List[String] []
--copy-attr-prefix
prefix to add to attributes to copy from bam
prefix to add to attributes to copy from bam
String ""
--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
--emit-ref-confidence / -ERC
Mode for emitting reference confidence scores (For Mutect2, this is a BETA feature)
The --emit-ref-confidence argument is an enumerated type (ReferenceConfidenceMode), which can have one of the following values:
- NONE
- Regular calling without emitting reference confidence calls.
- BP_RESOLUTION
- Reference model emitted site by site.
- GVCF
- Reference model emitted with condensed non-variant blocks, i.e. the GVCF format.
ReferenceConfidenceMode NONE
--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] []
--exclude-nan-scores
exclude nan scores
exclude NaN score records?
boolean false
--floor-blocks
Output the band lower bound for each GQ block regardless of the data it represents
boolean false
--flow-disallow-probs-larger-than-call
Cap probabilities of error to 1 relative to base call
boolean false
--flow-fill-empty-bins-value
Value to fill the zeros of the matrix with
double 0.001 [ [ -∞ ∞ ] ]
--flow-lump-probs
Should all probabilities of insertion or deletion in the flow be combined together
boolean false
--flow-matrix-mods
Modifications instructions to the read flow matrix. Format is src,dst{,src,dst}+. Example: 10,12,11,12 - these instructions will copy element 10 into 11 and 12
String null
--flow-probability-scaling-factor
probability scaling factor for (phred=10) for probability quantization
int 10 [ [ -∞ ∞ ] ]
--flow-probability-threshold
Lowest probability ratio to be used as an option
double 0.003 [ [ -∞ ∞ ] ]
--flow-quantization-bins
Number of bins for probability quantization
int 121 [ [ -∞ ∞ ] ]
--flow-remove-non-single-base-pair-indels
Should the probabilities of more then 1 indel be used
boolean false
--flow-remove-one-zero-probs
Remove probabilities of basecall of zero from non-zero genome
boolean false
--flow-report-insertion-or-deletion
Report either insertion or deletion, probability, not both
boolean false
--flow-retain-max-n-probs-base-format
Keep only hmer/2 probabilities (like in base format)
boolean false
--flow-symmetric-indel-probs
Should indel probabilities be symmetric in flow
boolean false
--flow-use-t0-tag
Use t0 tag if exists in the read to create flow matrix
boolean false
--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 ""
--gvcf-gq-bands / -GQB
Exclusive upper bounds for reference confidence GQ bands (must be in [1, 100] and specified in increasing order)
List[Integer] [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99]
--help / -h
display the help message
boolean false
--include-dup-reads
include duplicate reads
include duplicate read?
boolean false
--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] []
--keep-boundary-flows
prevent spreading of boundary flows.
boolean false
--keep-negatives
keep nevative scores?
keep negatives?
boolean false
--keep-supplementary-alignments
keep supplementary alignments ?
keep supplementary alignments?
boolean false
--lenient / -LE
Lenient processing of VCF files
boolean false
--limit-score
Limit value for score
maximum value for delta in score
double NaN [ [ -∞ ∞ ] ]
--mapping-feature
Kind of feaure being mapped
kind of feature we are mapping (looking for)
The --mapping-feature argument is an enumerated type (MappingFeatureEnum), which can have one of the following values:
- SNV
MappingFeatureEnum SNV
--max-score
threshold of score delta to for emitting (will be emitted if lower)
threshold of score delta to for emitting (will be emitted if lower)
double Infinity [ [ -∞ ∞ ] ]
--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-score
minimal threshold of score delta to for emitting (will be emitted if higher)
minimal threshold of score delta to for emitting (will be emitted if higher)
double -Infinity [ [ -∞ ∞ ] ]
--output / -O
File to which variants should be written
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
--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
--snv-identical-bases
number of bases that need to be identical before the snv
number of bases that need to be identical before the snv
int 1 [ [ -∞ ∞ ] ]
--snv-identical-bases-after
number of bases that need to be identical after the snv. 0 means same as number of bases before
number of bases that need to be identical after the snv
int 0 [ [ -∞ ∞ ] ]
--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
--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 4.4.0.0 built at Thu, 16 Mar 2023 15:00:37 -0400.
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