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VariantQC

Generate HTML summary report for a VCF

Category Variant Manipulation

Overview

VariantQC will generate a user-friendly HTML report that aggregates data from a VCF file by site, filter status, sample, and other stratifiers in order to provide various summary tables and graphs. In most cases the tables overlay bar graphs for numeric columns in order to help identify outliers. This tool is analogous to FASTQC or MultiQC, which provide similar HTML summary reports for different types of sequence data.

Usage examples:

Note: The public GATK Reference Bundle can be downloaded to provide example VCFs and a pre-indexed GRCh38 human genome build. See here for download instructions. We have also provide a small simplified VCF. You can download the VCF and download the VCF index, with can be used with the human_g1k_v37 genome.

Basic Usage, Without Pedigree:

 java -jar DISCVRSeq.jar VariantQC \
     -R human_g1k_v37.fasta \
     -V SimpleExample.vcf.gz \
     -O output.html

Report With Pedigree (required for gender information to display):

 java -jar DISCVRSeq.jar VariantQC \
     -R human_g1k_v37.fasta \
     -ped myPedigree.ped \
     -V input.vcf \
     -O output.html

Report With Multiple Input VCFs (not well tested). Note: you must supply a name for each VCF in the argument:

 java -jar DISCVRSeq.jar VariantQC \
     -R human_g1k_v37.fasta \
     -ped myPedigree.ped \
     -V:vcf1 input1.vcf \
     -V:vcf2 input2.vcf \
     -O output.html

Variant QC Output Report:

Below is an image of an example report, showing a VCF summarized by sample. The left-hand navigation allows the user to toggle between different stratifications (entire VCF, sample, contig, etc.). A complete example HTML report can be viewed here. The report contains a series of tables or graphs summarizing different aspects of the data. Below are the main types:

Variant Summary: A table displaying a summary of the total variants by type (SNP, insertion, deletion, MNP, etc.),
Variant Type: a bar plot summarizing variant by type (SNP, insertion, deletion, MNP, etc.)
Genotype Summary: A table summarizing the total called/non-called genotypes
SNP/Indel Summary:
Ti/Tv Data: A table displaying a summary of transition and transversion mutations in the dataset
Filter Type: A bar plot summarizing variants by filter

Advanced Usage:

VariantQC is designed to produce general-purpose reports applicable to a range of users; however, several mechanisms may make the output more useful to your data:

Write the raw output data to a separate file as JSON, which can be parsed separately:

 java -jar DISCVRSeq.jar VariantQC \
     -R human_g1k_v37.fasta \
     -V input.vcf \
     -rd output.json \
     -O output.html

Define additional reports to be included in the HTML report:

 java -jar DISCVRSeq.jar VariantQC \
     -R human_g1k_v37.fasta \
     -V input.vcf \
     --additionalReportFile reports.txt \
     -O output.html

Where reports.txt is a tab-delimited file with one report per line and no header. Comment lines can be included, beginning with '#'. This file has 4 columns:

Section label: Corresponds to the report group. This is typically 'Entire VCF', 'By Contig', etc.; however, any value can be used.
Report label: The title used for this report. For example: 'Variant Summary'
Stratifications: A comma-separated list of the stratifications to use when aggregating data. Allowable values are: VCF, Sample, Contig, and Filter
INFO field name: The name of the INFO field attribute to aggregate. This field must be of type character, string or integer. Note: this will produce a table summarizing the total variants for each level of this variable. Therefore a field with a wide range of possible values may not be appropriate to summarize in this manner. For example, while integer fields are support since in certain cases the value is bounded and will have a reasonable number of unique values.

Example Report File:

 By Sample	Example Report	Sample	PURPOSE
 By Contig	Example Report2	Sample,Contig	PURPOSE

Other Usage Suggestions:

Upstream processing of your VCF can enhance the value of the VariantQC report for your data. Our group routinely performs quality filtering on our VCFs, which saves information about the filter type in the FILTER field (see VariantFiltration). FilterType is used to stratify data in VariantQC, allowing us to view sample, VCF, or chromosome differences.

While VariantQC does not direct support automatic filtering/flagging of VCFs or samples based on thresholds, our group accomplishes this by writing a separate script to read the raw JSON output (see --rawData argument), and then applying our application-specific criteria.

Authors:

Ben Bimber, Ph.D.
Melissa Yan

Acknowledgements:

This tool internally uses GATK4's VariantEval to aggregate data, and borrows heavily from MultiQC for the HTML in the final report. We thank Philip Ewels for the use of MultiQC HTML/CSS/JS templates, and Chris Norman of the Broad Institute for assistance with VariantEval.

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 VariantQC.

WellformedReadFilter

VariantQC 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 the report should be written
--reference -R	null	Reference sequence file
--variant -V	[]	One or more VCF files containing variants
Optional Tool Arguments
--additionalReportFile -arf	null	This is an advanced usage feature. The user can define additional reports to display. Each report will read the value of the supplied INFO field, and make a table summarizing the number of variants for each value of this field. For example, if your VCF has the INFO field '', and this has values of , a table will be created summarizing the number of variants for each state. These will be stratified as defined in your file. Only INFO fields of type character, string and integer can be used. The file itself should be a tab-delimited file with one report per line, no header, and 4 columns: Section Label, Report Label, Stratification(s), and name of the INFO field to summarize. The TSV file is described in greater detail in the Advanced Usage section.
--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).
--contigsToRetain	[MT]	If --maxContigs is used, the first X contigs, are retained, sorted by length and preferentially retaining the longest contigs. This can be used to specify one or more additional contigs that are retained, even if they would otherwise be removed.
--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!
--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
--interval-merging-rule -imr	ALL	Interval merging rule for abutting intervals
--intervals -L	[]	One or more genomic intervals over which to operate
--maxContigs	40	Many VariantQC reports stratify data by contig. If the genome contains a large number of chromosomes, such as lots of unplaced contigs, this can bog down these reports in the final HTML file. As a default, VariantQC will only process the first 40 contigs, by length. This can be increased using this argument. See also --contigsToRetain
--pedigree -ped	null	Pedigree file for identifying Mendelian violations
--pedigreeValidationType -pedValidationType	STRICT	The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT
--rawData -rd	null	File to which the raw data will be written as JSON
--sites-only-vcf-output	false	If true, don't emit genotype fields when writing vcf file output.
--threads	1	The number of threads to use.
--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

--additionalReportFile / -arf

This is an advanced usage feature. The user can define additional reports to display. Each report will read the value of the supplied INFO field, and make a table summarizing the number of variants for each value of this field. For example, if your VCF has the INFO field '', and this has values of , a table will be created summarizing the number of variants for each state. These will be stratified as defined in your file. Only INFO fields of type character, string and integer can be used. The file itself should be a tab-delimited file with one report per line, no header, and 4 columns: Section Label, Report Label, Stratification(s), and name of the INFO field to summarize. The TSV file is described in greater detail in the Advanced Usage section.

File null

--arguments_file / NA

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 [ [ -∞ ∞ ] ]

--combine-variants-distance / NA

Maximum distance for variants to be grouped together

int 0 [ [ -∞ ∞ ] ]

--contigsToRetain / NA

If --maxContigs is used, the first X contigs, are retained, sorted by length and preferentially retaining the longest contigs. This can be used to specify one or more additional contigs that are retained, even if they would otherwise be removed.

List[String] [MT]

--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] []

--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 ""

--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 ∞ ] ]

--maxContigs / -maxContigs

Many VariantQC reports stratify data by contig. If the genome contains a large number of chromosomes, such as lots of unplaced contigs, this can bog down these reports in the final HTML file. As a default, VariantQC will only process the first 40 contigs, by length. This can be increased using this argument. See also --contigsToRetain

int 40 [ [ -∞ ∞ ] ]

--output / -O

File to which the report should be written

R String null

--pedigree / -ped

Pedigree file for identifying Mendelian violations

GATKPath null

--pedigreeValidationType / -pedValidationType

The strictness for validating the pedigree. Can be either STRICT or SILENT. Default is STRICT

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

STRICT
SILENT

PedigreeValidationType STRICT

--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean false

--rawData / -rd

File to which the raw data will be written as JSON

String null

--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: