Extract fields from a VCF file to a tab-delimited table
Category Variant Evaluation and Refinement
Overview
Extract fields from a VCF file to a tab-delimited tableThis 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.
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
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.
Additional Information
Read filters
This Read Filter is automatically applied to the data by the Engine before processing by VariantsToTable.
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.
--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] []
--asFieldsToTake / -ASF
The name of an allele-specific INFO field to be split if present
List[String] []
--asGenotypeFieldsToTake / -ASGF
The name of an allele-specific FORMAT field to be split if present
List[String] []
--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
--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
--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] []
--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] []
--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 ""
--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
--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] []
--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 ∞ ] ]
--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
--output / -O
File to which the tab-delimited table is written
R String 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
--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
--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
--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
--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 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.
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