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MergeVcfsAndGenotypes

Generate a merged VCF from one or more inputs

Category Variant Manipulation

Overview

MergeVcfsAndGenotypes is an adaptation of the Broad Institute GATK 3 tool CombineVariants. This is different from Picard tools MergeVcfs in that it will not only merge sites, but also merge genotypes.

MERGE: combines multiple variant records present at the same site in the different input sources into a single variant record in the output. If sample names overlap, then they are "uniquified" by default, which means a suffix is appended to make them unique. Note that in version 3.3, the automatic uniquifying was disabled (unintentionally), and required setting `-genotypeMergeOption UNIQUIFY` manually.
UNION: assumes that each ROD source represents the same set of samples (although this is not enforced). It uses the priority list (if provided) to emit a single record instance at every position represented in the input RODs.

By default, the input sets will be named variants, variants2, variants3, and so on. You can override this by providing an explicit name tag for each input, using the syntax " -V:name,format". Each input tagged in this way will be labeled as such in the output (i.e., set=name rather than set=variants2). For example, you could specify a set of control samples as " -V:control,vcf my_control_samples.vcf", and the resulting VCF records would contain the annotation "set=control" in the INFO field. It is strongly recommended to provide explicit names in this way when a rod priority list is provided.

MergeVcfsAndGenotypes will emit a record for every site that was present in any of your input VCF files, and will annotate (in the set attribute in the INFO field) whether the record had a PASS or FILTER status in each input VCF . In effect, MergeVcfsAndGenotypes always produces a union of the input VCFs. However, any part of the Venn of the merged VCFs can be extracted using JEXL expressions on the set attribute using SelectVariants and the 'set' attribute.

Important! If you select defined intervals, by default (in most GATK4-based walkers), any variant spanning the start site will be included If you are running scatter/gather jobs, this is probably not what you want. You can specify --ignore-variants-starting-outside-interval to force MergeVcfsAndGenotypes to only consider sites that start within the target intervals.

Input

Two or more variant sets to combine.

Output

A combined VCF.

Usage examples

Merge two separate callsets

 java -jar DISCVRseq.jar \
   -T MergeVcfsAndGenotypes \
   -R reference.fasta \
   --variant input1.vcf \
   --variant input2.vcf \
   --ignore-variants-starting-outside-interval \
   -L 1:1000-202029 \
   -O output.vcf \
   -genotypeMergeOption UNIQUIFY

Get the union of calls made on the same samples

 java -jar DISCVRseq.jar \
   -T MergeVcfsAndGenotypes \
   -R reference.fasta \
   --variant:foo input1.vcf \
   --variant:bar input2.vcf \
   -O output.vcf \
   -genotypeMergeOption PRIORITIZE \
   -priority foo,bar

Caveats

This tool is not intended to manipulate gVCFS! To combine GVCF files output for different samples by HaplotypeCaller, use CombineGVCFs.

Additional Information

Genome/Reference Files

Please note that if this tools uses a reference genome, that FASTA must be indexed with samtools and to have a sequence dictionary created with Picard. See here for more information

Read filters

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

WellformedReadFilter

MergeVcfsAndGenotypes 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	null	File to which variants should be written
--reference -R	null	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
--assumeIdenticalSamples	false	Assume input VCFs have identical sample sets and disjoint calls
--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!
--excludeNonVariants -env	false	Exclude sites where no variation is present after merging
--filteredAreUncalled	false	Treat filtered variants as uncalled
--filteredRecordsMergeType	KEEP_IF_ANY_UNFILTERED	Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields
--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.
--genotypeMergeOption	null	Determines how we should merge genotype records for samples shared across the VCF files
--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
--mergeInfoWithMaxAC	false	Use the INFO content of the record with the highest AC
--minimalVCF	false	Emit a sites-only file
--minimumN -minN	1	Minimum number of input files the site must be observed in to be included
--printComplexMerges	false	Emit interesting sites requiring complex compatibility merging to file
--priority_list -priority	null	Ordered list specifying priority for merging
--setKey	set	Key name for the set attribute
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--suppressCommandLineHeader	false	Do not output the command line to the header
--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.
--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	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
--combine-variants-distance	0	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	2147483647	Maximum distance for variants to be grouped together
--ref-padding	1	Number of bases on either side to expand spanning reference window
--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] []

--assumeIdenticalSamples / -assumeIdenticalSamples

Assume input VCFs have identical sample sets and disjoint calls
This option allows you to perform a simple merge (concatenation) to combine the VCFs, drastically reducing runtime. Note that in many cases where you think you want to use this option, you may want to check out the CatVariants tool instead, because CatVariants provides the same functionality, but does so even more efficiently.

boolean false

--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 / NA

Maximum distance for variants to be grouped together

int 0 [ [ -∞ ∞ ] ]

--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

--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] []

--excludeNonVariants / -env

Exclude sites where no variation is present after merging
Exclude sites that do not contain any called ALT alleles in the merged callset. The evaluation is made after the merging procedure is complete.

boolean false

--filteredAreUncalled / -filteredAreUncalled

Treat filtered variants as uncalled
If enabled, this flag causes filtered variants (i.e. variant records where the FILTER field is populated by something other than PASS or a dot) to be omitted from the output.

boolean false

--filteredRecordsMergeType / -filteredRecordsMergeType

Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields

The --filteredRecordsMergeType argument is an enumerated type (FilteredRecordMergeType), which can have one of the following values:

KEEP_IF_ANY_UNFILTERED
KEEP_IF_ALL_UNFILTERED
KEEP_UNCONDITIONAL

FilteredRecordMergeType KEEP_IF_ANY_UNFILTERED

--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. User must have storage.buckets.get permission on the bucket being accessed.

String ""

--genotypeMergeOption / -genotypeMergeOption

Determines how we should merge genotype records for samples shared across the VCF files

The --genotypeMergeOption argument is an enumerated type (GenotypeMergeType), which can have one of the following values:

UNIQUIFY
PRIORITIZE
UNSORTED
REQUIRE_UNIQUE

GenotypeMergeType null

--help / -h

display the help message

boolean false

--ignore-variants-starting-outside-interval / NA

Restrict variant output to sites that start within provided intervals (only applies when an interval is specified)

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
INTERSECTION

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-distance / NA

Maximum distance for variants to be grouped together

int 2147483647 [ [ -∞ ∞ ] ]

--max-variants-per-shard / NA

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

int 0 [ [ 0 ∞ ] ]

--mergeInfoWithMaxAC / -mergeInfoWithMaxAC

Use the INFO content of the record with the highest AC
By default, the INFO field of the merged variant record only contains the INFO field attributes for which all original overlapping records had the same values. Discordant attributes are therefore discarded. This flag allows you to override that behavior and simply copy over the INFO field contents of whichever record had the highest AC value.

boolean false

--minimalVCF / -minimalVCF

Emit a sites-only file
If this flag is enabled, the INFO, FORMAT and sample-level (genotype) fields will not be emitted to the output file.

boolean false

--minimumN / -minN

Minimum number of input files the site must be observed in to be included
Sites that are present in fewer than this number of inputs will be ignored. This is a convenient way to build a collection of common variants and exclude rare variants.

int 1 [ [ -∞ ∞ ] ]

--output / -O

File to which variants should be written

R File null

--printComplexMerges / -printComplexMerges

Emit interesting sites requiring complex compatibility merging to file

boolean false

--priority_list / -priority

Ordered list specifying priority for merging
Refers to the merging priority behavior described in the tool documentation regarding the choice of which record gets emitted when taking the union of variants that contain genotypes. The list must be passed as a comma-separated string listing the names of the variant input files. The list must be complete and include all variant inputs that are being provided to the tool. Use name tags for best results.

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[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 / NA

Number of bases on either side to expand spanning reference window

int 1 [ [ -∞ ∞ ] ]

--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 [ [ -∞ ∞ ] ]

--sequence-dictionary / -sequence-dictionary

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

GATKPath null

--setKey / -setKey

Key name for the set attribute
Key used in the INFO key=value tag emitted describing which set(s) the combined record came from (e.g. set=control). This provides the option to override the default naming, so instead of set=control you could have it be origin=control, or any other word you want that is not already an INFO field attribute. Set this to 'null' if you don't want the set attribute emitted at all.

String set

--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

--suppressCommandLineHeader / -suppressCommandLineHeader

Do not output the command line to the header
By default, this tool writes the command line that was used in the header of the output VCF file. This flag enables you to override that behavior . This is most often useful when combining variants for dozens or hundreds of smaller VCFs iteratively, to avoid cluttering the header with a lot of command lines.

boolean false