Extract fields from a VCF file to a tab-delimited table

Category Variant Evaluation and Refinement

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Overview

Extract fields from a VCF file to a tab-delimited table

This tool extracts specified fields for each variant in a VCF file to a tab-delimited table, which may be easier to work with than a VCF. By default, the tool only extracts PASS or . (unfiltered) variants in the VCF file. Filtered variants may be included in the output by adding the --show-filtered flag. The tool can extract both INFO (i.e. site-level) fields and FORMAT (i.e. sample-level) fields. If the tool is run without specifying any fields, it defaults to include all fields declared in the VCF header.

INFO/site-level fields

Use the `-F` argument to extract INFO fields; each field will occupy a single column in the output file. The field can be any standard VCF column (e.g. CHROM, ID, QUAL) or any annotation name in the INFO field (e.g. AC, AF). The tool also supports the following additional fields:

• EVENTLENGTH (length of the event)
• TRANSITION (1 for a bi-allelic transition (SNP), 0 for bi-allelic transversion (SNP), -1 for INDELs and multi-allelics)
• HET (count of het genotypes)
• HOM-REF (count of homozygous reference genotypes)
• HOM-VAR (count of homozygous variant genotypes)
• NO-CALL (count of no-call genotypes)
• TYPE (type of variant, possible values are NO_VARIATION, SNP, MNP, INDEL, SYMBOLIC, and MIXED
• VAR (count of non-reference genotypes)
• NSAMPLES (number of samples)
• NCALLED (number of called samples)
• MULTI-ALLELIC (is this variant multi-allelic? true/false)

Use the `-ASF` argument to extract allele-specific/per allele INFO fields and split them appropriately when splitting multi-allelic variants.

FORMAT/sample-level fields

Use the `-GF` argument to extract FORMAT/sample-level fields. The tool will create a new column per sample with the name "SAMPLE_NAME.FORMAT_FIELD_NAME" e.g. NA12877.GQ, NA12878.GQ.

Use the `-ASGF` argument to extract allele-specific/per allele FORMAT fields and split them appropriately when splitting multi-allelic variants. If AD is specified as an allele-specific genotype field the ref and alt counts will be given for each alt.

Inputs

• A VCF file to convert to a table

Output

A tab-delimited file containing the values of the requested fields in the VCF file.

Usage example

     gatk VariantsToTable \
     -V input.vcf \
     -F CHROM -F POS -F TYPE -GF AD \
     -O output.table
 

would produce a file that looks like:

     CHROM  POS        TYPE   HSCX1010N.AD  HSCX1010T.AD
     1      31782997   SNP    77,0          53,4
     1      40125052   SNP    97,0          92,7
     1      65068538   SNP    49,0          35,4
     1      111146235  SNP    69,1          77,4
 

     gatk VariantsToTable \
     -V input.vcf \
     -O output.table
 

would produce a file that includes all fields declared in the VCF header.

Notes

• It is common for certain annotations to be absent for some variants. By default, this tool will emit an NA for a missing annotation. If you prefer that the tool fail upon encountering a missing annotation, use the --error-if-missing-data flag.
• If multiple samples are present in the VCF, the genotype fields will be ordered alphabetically by sample name.
• Filtered sites are ignored by default. To include them in the output, use the --show-filtered flag.
• Allele-specific filtering is not yet supported. For PASS sites, all alleles will be given, regardless of their AS_FilterStatus.

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Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by VariantsToTable.

• WellformedReadFilter

VariantsToTable 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		File to which the tab-delimited table is written
--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
--asFieldsToTake  -ASF		The name of an allele-specific INFO field to be split if present
--asGenotypeFieldsToTake  -ASGF		The name of an allele-specific FORMAT field to be split if present
--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!
--fields  -F		The name of a standard VCF field or an INFO field to include in the output table
--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.
--genotype-fields  -GF		The name of a genotype field to include in the output table
--help  -h	false	display the help message
--interval-merging-rule  -imr	ALL	Interval merging rule for abutting intervals
--intervals  -L		One or more genomic intervals over which to operate
--reference  -R		Reference sequence
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--split-multi-allelic  -SMA	false	Split multi-allelic records into multiple lines
--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
--error-if-missing-data  -EMD	false	Fail on missing data
--moltenize	false	Produce molten output
--show-filtered  -raw	false	Include filtered records in the output
--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.

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--add-output-sam-program-record / -add-output-sam-program-record

If true, adds a PG tag to created SAM/BAM/CRAM files.

boolean  true

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--add-output-vcf-command-line / -add-output-vcf-command-line

If true, adds a command line header line to created VCF files.

boolean  true

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--arguments_file

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

List[File]  []

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--asFieldsToTake / -ASF

The name of an allele-specific INFO field to be split if present

List[String]  []

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--asGenotypeFieldsToTake / -ASGF

The name of an allele-specific FORMAT field to be split if present

List[String]  []

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--cloud-index-prefetch-buffer / -CIPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to cloudPrefetchBuffer if unset.

int  -1  [ [ -∞  ∞ ] ]

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--cloud-prefetch-buffer / -CPB

Size of the cloud-only prefetch buffer (in MB; 0 to disable).

int  40  [ [ -∞  ∞ ] ]

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--create-output-bam-index / -OBI

If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file.

boolean  true

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--create-output-bam-md5 / -OBM

If true, create a MD5 digest for any BAM/SAM/CRAM file created

boolean  false

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--create-output-variant-index / -OVI

If true, create a VCF index when writing a coordinate-sorted VCF file.

boolean  true

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--create-output-variant-md5 / -OVM

If true, create a a MD5 digest any VCF file created.

boolean  false

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--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

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--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

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--error-if-missing-data / -EMD

Fail on missing data
By default, this tool will write NA for missing data. Turn on this flag, and the tool will throw an error and exit if it encounters missing data.

boolean  false

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--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]  []

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--fields / -F

The name of a standard VCF field or an INFO field to include in the output table
Any standard VCF column (CHROM, ID, QUAL) or any annotation name in the INFO field (e.g., -F AC) to include in the output table. To capture FORMAT field values, see the -GF argument. This argument accepts any number of inputs e.g. -F CHROM -F POS

List[String]  []

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--gatk-config-file

A configuration file to use with the GATK.

String  null

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--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  [ [ -∞  ∞ ] ]

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--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  ""

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--genotype-fields / -GF

The name of a genotype field to include in the output table
Any annotation name in the FORMAT field (e.g., GQ, PL) to include in the output table. This argument accepts any number of inputs e.g. -GF GQ -GF PL

List[String]  []

---

--help / -h

display the help message

boolean  false

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--input / -I

BAM/SAM/CRAM file containing reads

List[GATKPath]  []

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--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  [ [ -∞  ∞ ] ]

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--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

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--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  [ [ -∞  ∞ ] ]

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--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

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--intervals / -L

One or more genomic intervals over which to operate

List[String]  []

---

--lenient / -LE

Lenient processing of VCF files

boolean  false

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--max-variants-per-shard

If non-zero, partitions VCF output into shards, each containing up to the given number of records.

int  0  [ [ 0  ∞ ] ]

---

--moltenize / -moltenize

Produce molten output
Use this flag to emit each field within a variant on a separate line. The resulting table will have four columns: RecordID, Sample, Variable, and Value. Variable refers to the field name, Value to the value of the field. The tool prints "site" under Sample column for an INFO or standard field. Example: -F CHROM -GF AD will print the following table RecordID Sample Variable Value 1 site CHROM 20 1 NA12878 AD 36,28 2 site CHROM 20 2 NA12878 AD 26,27 3 site CHROM 20

boolean  false

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--output / -O

File to which the tab-delimited table is written

R String  null

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--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

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--reference / -R

Reference sequence

GATKPath  null

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--seconds-between-progress-updates / -seconds-between-progress-updates

Output traversal statistics every time this many seconds elapse

double  10.0  [ [ -∞  ∞ ] ]

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--sequence-dictionary / -sequence-dictionary

Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a .dict file.

GATKPath  null

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--show-filtered / -raw

Include filtered records in the output
By default this tool only emits values for records where the FILTER field is either PASS or . (unfiltered). Turn on this flag to emit values regardless of the value of the FILTER field.

boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--sites-only-vcf-output

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

boolean  false

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--split-multi-allelic / -SMA

Split multi-allelic records into multiple lines
By default, a variant record with multiple ALT alleles will be summarized in one line, with per alt-allele fields (e.g. allele depth) separated by commas. This may cause difficulty when the table is loaded by an R script, for example. Use this flag to write multi-allelic records on separate lines of output. Fields that are not allele-specific will be duplicated.

boolean  false

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--tmp-dir

Temp directory to use.

GATKPath  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--variant / -V

A VCF file containing variants

R GATKPath  null

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--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

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--version

display the version number for this tool

boolean  false

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GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.