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overview

selects variants from a vcf source. often, a vcf containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like igv, etc.). selectvariants can be used for this purpose. given a single vcf file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). variants can be further selected by specifying criteria for inclusion, i.e. "dp > 1000" (depth of coverage greater than 1000x), "af < 0.25" (sites with allele frequency less than 0.25). these jexl expressions are documented in the using jexl expressions section (http://www.broadinstitute.org/gatk/guide/article?id=1255). one can optionally include concordance or discordance tracks for use in selecting overlapping variants.

output variants that were also called in this comparison track. a site is considered concordant if (1) we are not looking for specific samples and there is a variant called in both the variant and concordance tracks or (2) every sample present in the variant track is present in the concordance track and they have the sample genotype call. --concordance binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--discordance / -disc ( rodbinding[variantcontext] with default value none )

output variants that were not called in this comparison track. a site is considered discordant if there exists some sample in the variant track that has a non-reference genotype and either the site isn't present in this track, the sample isn't present in this track, or the sample is called reference in this track. --discordance binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--exclude_sample_file / -xl_sf ( set[file] with default value [] )

file containing a list of samples (one per line) to exclude. can be specified multiple times. note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.

--exclude_sample_name / -xl_sn ( set[string] with default value [] )

exclude genotypes from this sample. can be specified multiple times. note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.

--excludefiltered / -ef ( boolean with default value false )

don't include filtered loci in the analysis.

--excludenonvariants / -env ( boolean with default value false )

don't include loci found to be non-variant after the subsetting procedure.

--keepids / -ids ( file )

only emit sites whose id is found in this file (one id per line). if provided, we will only include variants whose id field is present in this list of ids. the matching is exact string matching. the file format is just one id per line

file to which variants should be written.

regular expression to select many samples from the rod tracks provided. can be specified multiple times.

--sample_file / -sf ( set[file] )

file containing a list of samples (one per line) to include. can be specified multiple times.

--sample_name / -sn ( set[string] with default value [] )

include genotypes from this sample. can be specified multiple times.

--select_expressions / -select ( arraylist[string] with default value [] )

one or more criteria to use when selecting the data. note that these expressions are evaluated *after* the specified samples are extracted and the info field annotations are updated.

select only a certain type of variants from the input file. valid types are indel, snp, mixed, mnp, symbolic, no_variation. can be specified multiple times. this argument select particular kinds of variants out of a list. if left empty, there is no type selection and all variant types are considered for other selection criteria. when specified one or more times, a particular type of variant is selected.

--variant / -v ( required rodbinding[variantcontext] )

input vcf file. variants from this vcf file are used by this tool as input. the file must at least contain the standard vcf header lines, but can be empty (i.e., no variants are contained in the file). --variant binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

examples

 select two samples out of a vcf with many samples: 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -sn sample_a_parc 
   -sn sample_b_actg
 



select two samples and any sample that matches a regular expression:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -sn sample_1_parc 
   -sn sample_1_actg 
   -se 'sample. parc'




select any sample that matches a regular expression and sites where the qd annotation is more than 10:


 java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -se 'sample. parc'
   -select "qd > 10.0"
 



select a sample and exclude non-variant loci and filtered loci:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -sn sample_1_actg 
   -env 
   -ef
 



select a sample and restrict the output vcf to a set of intervals:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -l /path/to/my.interval_list 
   -sn sample_1_actg
 



select all calls missed in my vcf, but present in hapmap (useful to take a look at why these variants weren't called by this dataset):
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant hapmap.vcf 
   --discordance mycalls.vcf
   -o output.vcf 
   -sn mysample




select all calls made by both mycalls and hiscalls (useful to take a look at what is consistent between the two callers):


 java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant mycalls.vcf 
   --concordance hiscalls.vcf
   -o output.vcf 
   -sn mysample




generating a vcf of all the variants that are mendelian violations:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -bed family.ped 
   -mvq 50 
   -o violations.vcf
 



creating a set with 50% of the total number of variants in the variant vcf:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -fraction 0.5
 



select only indels from a vcf:
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -selecttype indel




select only multi-allelic snps and mnps from a vcf (i.e. snps with more than one allele listed in the alt column):
 

java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t selectvariants 
   --variant input.vcf 
   -o output.vcf 
   -selecttype snp -selecttype mnp 
   -restrictallelesto multiallelic



===============================java表达式2lw12nx4====================================

java表达式2lw12nx4（jexl，主要用于variantfiltration 和 selectvariants）

"qual > 30.0"

java -xmx4g -jar genomeanalysistk.jar -t selectvariants -r b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.getgenotype("na12878").ishomref()'

! vc.getgenotype("01-0263").ishomref() && (vc.getid() == null || vc.getid().equals(".")) && af > 0.25 && af < 1.0 && vc.isnotfiltered() && vc.issnp() -o 01-0263.high_freq_novels.vcf -sn 01-0263

java -xmx4g -jar genomeanalysistk.jar -t selectvariants -r b37/human_g1k_v37.fasta --variant my.vcf -select 'db'

java -xmx4g -jar genomeanalysistk.jar -t selectvariants -r b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.hasattribute("db")'

java -xmx4g -jar genomeanalysistk.jar -t selectvariants -r b37/human_g1k_v37.fasta --variant my.vcf -select 'vc.getgenotype("na12878").getad().0 > 10'

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combinevariants combines vcf records from different sources. any (unique) name can be used to bind your rod data and any number of sources can be input. this tool currently supports two different combination types for each of variants (the first 8 fields of the vcf) and genotypes (the rest). merge: combines multiple records into a single one; if sample names overlap then they are uniquified. union: assumes each rod represents the same set of samples (although this is not enforced); using the priority list (if provided), it emits a single record instance at every position represented in the rods. combinevariants will include a record at every site in all of your input vcf files, and annotate which input rod bindings the record is present, pass, or filtered in in the set attribute in the info field. in effect, combinevariants always produces a union of the input vcfs. however, any part of the venn of the n merged vcfs can be exacted using jexl expressions on the set attribute using selectvariants. if you want to extract just the records in common between two vcfs, you would first run combinevariants on the two files to generate a single vcf and then run selectvariants to extract the common records with -select 'set == "intersection"', as worked out in the detailed example in the documentation guide. note that combinevariants supports multi-threaded parallelism (8/15/12). this is particularly useful when converting from vcf to bcf2, which can be expensive. in this case each thread spends cpu time doing the conversion, and the gatk engine is smart enough to merge the partial bcf2 blocks together efficiency. however, since this merge runs in only one thread, you can quickly reach diminishing returns with the number of parallel threads. -nt 4 works well but -nt 8 may be too much. some fine details about the merging algorithm:

• as of gatk 2.1, when merging multiple vcf records at a site, the combined vcf record has the qual of the first vcf record with a non-missing qual value. the previous behavior was to take the max qual, which resulted in sometime strange downstream confusion

input

one or more variant sets to combine.

output

a combined vcf.

examples

 java -xmx2g -jar genomeanalysistk.jar 
   -r ref.fasta 
   -t combinevariants 
   --variant input1.vcf 
   --variant input2.vcf 
   -o output.vcf 
   -genotypemergeoptions uniquify
 java -xmx2g -jar 



genomeanalysistk.jar 
   -r ref.fasta 
   -t combinevariants 
   --variant:foo input1.vcf 
   --variant:bar input2.vcf 
   -o output.vcf 
   -genotypemergeoptions prioritize
   -priority foo,bar

参数

--assumeidenticalsamples / -assumeidenticalsamples ( boolean with default value false )

if true, assume input vcfs have identical sample sets and disjoint calls. this option allows the user to perform a simple merge (concatenation) to combine the vcfs, drastically reducing the runtime..

--filteredareuncalled / -filteredareuncalled ( boolean with default value false )

if true, then filtered vcfs are treated as uncalled, so that filtered set annotations don't appear in the combined vcf.

--filteredrecordsmergetype / -filteredrecordsmergetype ( filteredrecordmergetype with default value keep_if_any_unfiltered )

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

union - leaves the record if any record is unfiltered.

keep_if_all_unfiltered

requires all records present at site to be unfiltered. vcf files that don't contain the record don't influence this.

keep_unconditional

if any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset.

--genotypemergeoption / -genotypemergeoptions ( genotypemergetype )

determines how we should merge genotype records for samples shared across the rod files.
the --genotypemergeoption argument is an enumerated type (genotypemergetype), which can have one of the following values:

uniquify

make all sample genotypes unique by file. each sample shared across rods gets named sample.rod.

prioritize

take genotypes in priority order (see the priority argument).

unsorted

take the genotypes in any order.

require_unique

require that all samples/genotypes be unique between all inputs.

--mergeinfowithmaxac / -mergeinfowithmaxac ( boolean with default value false )

if true, when vcf records overlap the info field is taken from the one with the max ac instead of only taking the fields which are identical across the overlapping records..

--minimalvcf / -minimalvcf ( boolean with default value false )

if true, then the output vcf will contain no info or genotype format fields. used to generate a sites-only file.

--minimumn / -minn ( int with default value 1 )

combine variants and output site only if the variant is present in at least n input files..

--out / -o ( variantcontextwriter with default value stdout )

file to which variants should be written.

--printcomplexmerges / -printcomplexmerges ( boolean with default value false )

print out interesting sites requiring complex compatibility merging.

--rod_priority_list / -priority ( string )

a comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted. used when taking the union of variants that contain genotypes. a complete priority list must be provided.

--setkey / -setkey ( string with default value set )

key used in the info key=value tag emitted describing which set the combined vcf record came from. set to 'null' if you don't want the set field emitted.

--suppresscommandlineheader / -suppresscommandlineheader ( boolean with default value false )

if true, do not output the header containing the command line used. this option allows the suppression of the command line in the vcf header. this is most often usefully when combining variants for dozens or hundreds of smaller vcfs.

--variant / -v ( required list[rodbinding[variantcontext]] )

input vcf file. the vcf files to merge together variants can take any number of arguments on the command line. each -v argument will be included in the final merged output vcf. if no explicit name is provided, the -v arguments will be named using the default algorithm: variants, variants2, variants3, etc. the user can override this by providing an explicit name -v:name,vcf for each -v argument, and each named argument will be labeled as such in the output (i.e., set=name rather than set=variants2). the order of arguments does not matter unless except for the naming, so if you provide an rod priority list and no explicit names than variants, variants2, etc are technically order dependent. it is strongly recommended to provide explicit names when a rod priority list is provided. --variant binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

general-purpose tool for variant evaluation (% in dbsnp, genotype concordance, ti/tv ratios, and a lot more)

given a variant callset, it is common to calculate various quality control metrics. these metrics include the number of raw or filtered snp counts; ratio of transition mutations to transversions; concordance of a particular sample's calls to a genotyping chip; number of singletons per sample; etc. furthermore, it is often useful to stratify these metrics by various criteria like functional class (missense, nonsense, silent), whether the site is cpg site, the amino acid degeneracy of the site, etc. varianteval facilitates these calculations in two ways: by providing several built-in evaluation and stratification modules, and by providing a framework that permits the easy development of new evaluation and stratification modules.

input

one or more variant sets to evaluate plus any number of comparison sets.

output

evaluation tables detailing the results of the eval modules which were applied.

参数

--ancestralalignments / -aa ( file )

fasta file with ancestral alleles.

--comp / -comp ( list[rodbinding[variantcontext]] with default value [] )

input comparison file(s). the variant file(s) to compare against. --comp binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--dbsnp / -d ( rodbinding[variantcontext] with default value none )

dbsnp file. dbsnp comparison vcf. by default, the dbsnp file is used to specify the set of "known" variants. other sets can be specified with the -knownname (--known_names) argument. --dbsnp binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--donotuseallstandardmodules / -noev ( boolean with default value false )

do not use the standard modules by default (instead, only those that are specified with the -ev option).

--eval / -eval ( required list[rodbinding[variantcontext]] )

input evaluation file(s). the variant file(s) to evaluate. --eval binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--evalmodule / -ev ( string[] with default value [] )

one or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noev is specified). see the -list argument to view available modules.

--goldstandard / -gold ( rodbinding[variantcontext] with default value none )

evaluations that count calls at sites of true variation (e.g., indel calls) will use this argument as their gold standard for comparison. some analyses want to count overlap not with dbsnp (which is in general very open) but actually want to itemize their overlap specifically with a set of gold standard sites such as hapmap, omni, or the gold standard indels. this argument provides a mechanism for communicating which file to use --goldstandard binds reference ordered data. this argument supports rod files of the following types: bcf2, vcf, vcf3

--keepac0 / -keepac0 ( boolean with default value false )

if provided, modules that track polymorphic sites will not require that a site have ac > 0 when the input eval has genotypes.

--known_names / -knownname ( hashset[string] with default value [] )

name of rod bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets. list of rod tracks to be used for specifying "known" variants other than dbsnp.

--knowncnvs / -knowncnvs ( intervalbinding[feature] )

file containing tribble-readable features describing a known list of copy number variants. file containing tribble-readable features containing known cnvs. for use with variantsummary table.

--list / -ls ( boolean with default value false )

list the available eval modules and exit. note that the --list argument requires a fully resolved and correct command-line to work.

--mergeevals / -mergeevals ( boolean with default value false )

if provided, all -eval tracks will be merged into a single eval track. if true, varianteval will treat -eval 1 -eval 2 as separate tracks from the same underlying variant set, and evaluate the union of the results. useful when you want to do -eval chr1.vcf -eval chr2.vcf etc.

--minphasequality / -mpq ( double with default value 10.0 )

minimum phasing quality.

-mvq / --mendelianviolationqualthreshold ( double with default value 50.0 )

minimum genotype qual score for each trio member required to accept a site as a violation. default is 50..

-nost / --donotuseallstandardstratifications ( boolean with default value false )

do not use the standard stratification modules by default (instead, only those that are specified with the -s option).

--out / -o ( printstream with default value stdout )

an output file created by the walker. will overwrite contents if file exists.

--requirestrictallelematch / -strict ( boolean with default value false )

if provided only comp and eval tracks with exactly matching reference and alternate alleles will be counted as overlapping.

--sample / -sn ( set[string] )

derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context.

--sampleploidy / -ploidy ( int with default value 2 )

per-sample ploidy (number of chromosomes per sample).

--select_exps / -select ( arraylist[string] with default value [] )

one or more stratifications to use when evaluating the data.

--select_names / -selectname ( arraylist[string] with default value [] )

names to use for the list of stratifications (must be a 1-to-1 mapping).

--stratificationmodule / -st ( string[] with default value [] )

one or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -nos is specified).

--stratintervals / -stratintervals ( intervalbinding[feature] )

file containing tribble-readable features for the intervalstratificiation. file containing tribble-readable features for the intervalstratificiation