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<!doctype html>

<html>

<head>

<title>VCFtools</title>

<!--[if lt IE 9]>

<![endif]-->

</head>

<body>

<h1 class="header">VCFtools</h1>

A set of tools written in Perl and C++ for working with VCF files.

<ul>

<li><a href="examples.html">Documentation</a></li>

<li class="download"><a class="buttons" href="https://github.com/vcftools/vcftools/zipball/master">Download ZIP</a></li>

<li class="download"><a class="buttons" href="https://github.com/vcftools/vcftools/tarball/master">Download TAR</a></li>

<li><a class="buttons github" href="https://github.com/vcftools/vcftools">View On GitHub</a></li>

</ul>

</header>

<a href="#SYNOPSIS">SYNOPSIS</a>

<a href="#DESCRIPTION">DESCRIPTION</a>

<a href="#EXAMPLES">EXAMPLES</a>

<a href="#BASIC OPTIONS">BASIC OPTIONS</a>

<a href="#SITE FILTERING OPTIONS">SITE FILTERING OPTIONS</a>

<a href="#INDIVIDUAL FILTERING OPTIONS">INDIVIDUAL FILTERING OPTIONS</a>

<a href="#GENOTYPE FILTERING OPTIONS">GENOTYPE FILTERING OPTIONS</a>

<a href="#OUTPUT OPTIONS">OUTPUT OPTIONS</a>

<a href="#COMPARISON OPTIONS">COMPARISON OPTIONS</a>

<a href="#AUTHORS">AUTHORS</a>

<hr>

<h2>NAME

</h2>

vcftools

v0.1.13 − Utilities for the variant call format (VCF)

and binary variant call format (BCF)

<h2>SYNOPSIS

</h2>

vcftools

[ --vcf FILE | --gzvcf FILE | --bcf

FILE] [ --out OUTPUT PREFIX ] [ FILTERING OPTIONS ] [

OUTPUT OPTIONS ]

<h2>DESCRIPTION

</h2>

vcftools is a

suite of functions for use on genetic variation data in the

form of VCF and BCF files. The tools provided will be used

mainly to summarize data, run calculations on data, filter

out data, and convert data into other useful file

formats.

<h2>EXAMPLES

</h2>

Output allele

frequency for all sites in the input vcf file from

chromosome 1

vcftools --gzvcf

input_file.vcf.gz --freq --chr 1 --out chr1_analysis

Output a new

vcf file from the input vcf file that removes any indel

sites

vcftools --vcf

input_file.vcf --remove-indels --recode --recode-INFO-all

--out SNPs_only

Output file

comparing the sites in two vcf files

vcftools --gzvcf

input_file1.vcf.gz --gzdiff input_file2.vcf.gz --diff-site

--out in1_v_in2

Output a new

vcf file to standard out without any sites that have a

filter tag, then compress it with gzip

vcftools --gzvcf

input_file.vcf.gz --remove-filtered-all --recode --stdout |

gzip -c > output_PASS_only.vcf.gz

Output a

Hardy-Weinberg p-value for every site in the bcf file that

does not have any missing genotypes

vcftools --bcf

input_file.bcf --hardy --max-missing 1.0 --out

output_noMissing

Output

nucleotide diversity at a list of positions

zcat input_file.vcf.gz |

vcftools --vcf - --site-pi --positions SNP_list.txt

--out nucleotide_diversity

<h2>BASIC OPTIONS

</h2>

These options

are used to specify the input and output files.

INPUT FILE

OPTIONS

--vcf

<input_filename>

This option defines the VCF

file to be processed. VCFtools expects files in VCF format

v4.0, v4.1 or v4.2. The latter two are supported with some

small limitations. If the user provides a dash character

’-’ as a file name, the program expects a VCF

file to be piped in through standard in.

--gzvcf

<input_filename>

This option can be used in

place of the --vcf option to read compressed (gzipped) VCF

files directly.

--bcf

<input_filename>

This option can be used in

place of the --vcf option to read BCF2 files directly. You

do not need to specify if this file is compressed with BGZF

encoding. If the user provides a dash character

’-’ as a file name, the program expects a BCF2

file to be piped in through standard in.

OUTPUT FILE

OPTIONS

--out

<output_prefix>

This option defines the output

filename prefix for all files generated by vcftools. For

example, if <prefix> is set to output_filename, then

all output files will be of the form output_filename.*** .

If this option is omitted, all output files will have the

prefix "out." in the current working

directory.

--stdout

-c

These options direct the

vcftools output to standard out so it can be piped into

another program or written directly to a filename of choice.

However, a select few output functions cannot be written to

standard out.

--temp

<temporary_directory>

This option can be used to

redirect any temporary files that vcftools creates into a

specified directory.

<h2>SITE FILTERING OPTIONS

</h2>

These options

are used to include or exclude certain sites from any

analysis being performed by the program.

POSITION

FILTERING

--chr

--not-chr <chromosome>

Includes or excludes sites with

indentifiers matching <chromosome>. These options may

be used multiple times to include or exclude more than one

chromosome.

--from-bp

--to-bp <integer>

These options specify a lower

bound and upper bound for a range of sites to be processed.

Sites with positions less than or greater than these values

will be excluded. These options can only be used in

conjunction with a single usage of --chr. Using one of these

does not require use of the other.

--positions

--exclude-positions <filename>

Include or exclude a set of

sites on the basis of a list of positions in a file. Each

line of the input file should contain a (tab-separated)

chromosome and position. The file can have comment lines

that start with a "#", they will be ignored.

--positions-overlap

--exclude-positions-overlap <filename>

Include or exclude a set of

sites on the basis of the reference allele overlapping with

a list of positions in a file. Each line of the input file

should contain a (tab-separated) chromosome and position.

The file can have comment lines that start with a

"#", they will be ignored.

--bed

--exclude-bed <filename>

Include or exclude a set of

sites on the basis of a BED file. Only the first three

columns (chrom, chromStart and chromEnd) are required. The

BED file is expected to have a header line. A site will be

kept or excluded if any part of any allele (REF or ALT) at a

site is within the range of one of the BED entries.

--thin

Thin sites so that no two sites

are within the specified distance from one another.

--mask

--invert-mask <filename>

--mask-min <integer>

These options are used to

specify a FASTA-like mask file to filter with. The mask file

contains a sequence of integer digits (between 0 and 9) for

each position on a chromosome that specify if a site at that

position should be filtered or not.

An example mask file would look like:

>1

0000011111222...

>2

2222211111000...

In this example, sites in the

VCF file located within the first 5 bases of the start of

chromosome 1 would be kept, whereas sites at position 6

onwards would be filtered out. And sites after the 11th

position on chromosome 2 would be filtered out as well.

The "--invert-mask" option takes the same format

mask file as the "--mask" option, however it

inverts the mask file before filtering with it.

And the "--mask-min" option specifies a threshold

mask value between 0 and 9 to filter positions by. The

default threshold is 0, meaning only sites with that value

or lower will be kept.

SITE ID

FILTERING

--snp

Include SNP(s) with matching ID

(e.g. a dbSNP rsID). This command can be used multiple times

in order to include more than one SNP.

--snps

--exclude <filename>

Include or exclude a list of

SNPs given in a file. The file should contain a list of SNP

IDs (e.g. dbSNP rsIDs), with one ID per line. No header line

is expected.

VARIANT TYPE

FILTERING

--keep-only-indels

--remove-indels

Include or exclude sites that

contain an indel. For these options "indel" means

any variant that alters the length of the REF allele.

FILTER FLAG

FILTERING

--remove-filtered-all

Removes all sites with a FILTER

flag other than PASS.

--keep-filtered

--remove-filtered <string>

Includes or excludes all sites

marked with a specific FILTER flag. These options may be

used more than once to specify multiple FILTER flags.

INFO FIELD

FILTERING

--keep-INFO

--remove-INFO <string>

Includes or excludes all sites

with a specific INFO flag. These options only filter on the

presence of the flag and not its value. These options can be

used multiple times to specify multiple INFO flags.

ALLELE

FILTERING

--maf

<float>

--max-maf <float>

Include only sites with a Minor

Allele Frequency greater than or equal to the

"--maf" value and less than or equal to the

"--max-maf" value. One of these options may be

used without the other. Allele frequency is defined as the

number of times an allele appears over all individuals at

that site, divided by the total number of non-missing

alleles at that site.

--non-ref-af

<float>

--max-non-ref-af <float>

--non-ref-ac <integer>

--max-non-ref-ac <integer>

--non-ref-af-any

<float>

--max-non-ref-af-any <float>

--non-ref-ac-any <integer>

--max-non-ref-ac-any <integer>

Include only sites with all

Non-Reference (ALT) Allele Frequencies (af) or Counts (ac)

within the range specified, and including the specified

value. The default options require all alleles to

meet the specified criteria, whereas the options appended

with "any" require only one allele to meet the

criteria. The Allele frequency is defined as the number of

times an allele appears over all individuals at that site,

divided by the total number of non-missing alleles at that

site.

--mac

--max-mac <integer>

Include only sites with Minor

Allele Count greater than or equal to the "--mac"

value and less than or equal to the "--max-mac"

value. One of these options may be used without the other.

Allele count is simply the number of times that allele

appears over all individuals at that site.

--min-alleles

--max-alleles <integer>

Include only sites with a

number of alleles greater than or equal to the

"--min-alleles" value and less than or equal to

the "--max-alleles" value. One of these options

may be used without the other.

For example, to include only bi-allelic sites, one could

use:

vcftools --vcf file1.vcf

--min-alleles 2 --max-alleles 2

GENOTYPE

VALUE FILTERING

--min-meanDP

<float>

--max-meanDP <float>

Includes only sites with mean

depth values (over all included individuals) greater than or

equal to the "--min-meanDP" value and less than or

equal to the "--max-meanDP" value. One of these

options may be used without the other. These options require

that the "DP" FORMAT tag is included for each

site.

--hwe

<float>

Assesses sites for

Hardy-Weinberg Equilibrium using an exact test, as defined

by Wigginton, Cutler and Abecasis (2005). Sites with a

p-value below the threshold defined by this option are taken

to be out of HWE, and therefore excluded.

--max-missing

<float>

Exclude sites on the basis of

the proportion of missing data (defined to be between 0 and

1, where 0 allows sites that are completely missing and 1

indicates no missing data allowed).

--max-missing-count

Exclude sites with more than

this number of missing genotypes over all individuals.

--phased

Excludes all sites that contain

unphased genotypes.

MISCELLANEOUS

FILTERING

--minQ

<float>

Includes only sites with

Quality value above this threshold.

<h2>INDIVIDUAL FILTERING OPTIONS

</h2>

These options

are used to include or exclude certain individuals from any

analysis being performed by the program.

--indv

--remove-indv <string>

Specify an individual to be

kept or removed from the analysis. This option can be used

multiple times to specify multiple individuals. If both

options are specified, then the "--indv" option is

executed before the "--remove-indv option".

--keep

--remove <filename>

Provide files containing a list

of individuals to either include or exclude in subsequent

analysis. Each individual ID (as defined in the VCF

headerline) should be included on a separate line. If both

options are used, then the "--keep" option is

executed before the "--remove" option. When

multiple files are provided, the union of individuals from

all keep files subtracted by the union of individuals from

all remove files are kept. No header line is expected.

--max-indv

Randomly thins individuals so

that only the specified number are retained.

<h2>GENOTYPE FILTERING OPTIONS

</h2>

These options

are used to exclude genotypes from any analysis being

performed by the program. If excluded, these values will be

treated as missing.

--remove-filtered-geno-all

Excludes all genotypes with a

FILTER flag not equal to "." (a missing value) or

PASS.

--remove-filtered-geno

Excludes genotypes with a

specific FILTER flag.

--minGQ

<float>

Exclude all genotypes with a

quality below the threshold specified. This option requires

that the "GQ" FORMAT tag is specified for all

sites.

--minDP

<float>

--maxDP <float>

Includes only genotypes greater

than or equal to the "--minDP" value and less than

or equal to the "--maxDP" value. This option

requires that the "DP" FORMAT tag is specified for

all sites.

<h2>OUTPUT OPTIONS

</h2>

These options

specify which analyses or conversions to perform on the data

that passed through all specified filters.

OUTPUT

ALLELE STATISTICS

--freq

--freq2

Outputs the allele frequency

for each site in a file with the suffix ".frq".

The second option is used to suppress output of any

information about the alleles.

--counts

--counts2

Outputs the raw allele counts

for each site in a file with the suffix

".frq.count". The second option is used to

suppress output of any information about the alleles.

--derived

For use with the previous four

frequency and count options only. Re-orders the output file

columns so that the ancestral allele appears first. This

option relies on the ancestral allele being specified in the

VCF file using the AA tag in the INFO field.

OUTPUT DEPTH

STATISTICS

--depth

Generates a file containing the

mean depth per individual. This file has the suffix

".idepth".

--site-depth

Generates a file containing the

depth per site summed across all individuals. This output

file has the suffix ".ldepth".

--site-mean-depth

Generates a file containing the

mean depth per site averaged across all individuals. This

output file has the suffix ".ldepth.mean".

--geno-depth

Generates a (possibly very

large) file containing the depth for each genotype in the

VCF file. Missing entries are given the value -1. The file

has the suffix ".gdepth".

OUTPUT LD

STATISTICS

--hap-r2

Outputs a file reporting the

r2, D, and D’ statistics using phased haplotypes.

These are the traditional measures of LD often reported in

the population genetics literature. The output file has the

suffix ".hap.ld". This option assumes that the VCF

input file has phased haplotypes.

--geno-r2

Calculates the squared

correlation coefficient between genotypes encoded as 0, 1

and 2 to represent the number of non-reference alleles in

each individual. This is the same as the LD measure reported

by PLINK. The D and D’ statistics are only available

for phased genotypes. The output file has the suffix

".geno.ld".

--geno-chisq

If your data contains sites

with more than two alleles, then this option can be used to

test for genotype independence via the chi-squared

statistic. The output file has the suffix

".geno.chisq".

--hap-r2-positions

--geno-r2-positions <positions list

file>

Outputs a file reporting the r2

statistics of the sites contained in the provided file

verses all other sites. The output files have the suffix

".list.hap.ld" or ".list.geno.ld",

depending on which option is used.

--ld-window

This optional parameter defines

the maximum number of SNPs between the SNPs being tested for

LD in the "--hap-r2", "--geno-r2", and

"--geno-chisq" functions.

--ld-window-bp

This optional parameter defines

the maximum number of physical bases between the SNPs being

tested for LD in the "--hap-r2",

"--geno-r2", and "--geno-chisq"

functions.

--ld-window-min

This optional parameter defines

the minimum number of SNPs between the SNPs being tested for

LD in the "--hap-r2", "--geno-r2", and

"--geno-chisq" functions.

--ld-window-bp-min

This optional parameter defines

the minimum number of physical bases between the SNPs being

tested for LD in the "--hap-r2",

"--geno-r2", and "--geno-chisq"

functions.

--min-r2

<float>

This optional parameter sets a

minimum value for r2, below which the LD statistic is not

reported by the "--hap-r2", "--geno-r2",

and "--geno-chisq" functions.

--interchrom-hap-r2

--interchrom-geno-r2

Outputs a file reporting the r2

statistics for sites on different chromosomes. The output

files have the suffix ".interchrom.hap.ld" or

".interchrom.geno.ld", depending on the option

used.

OUTPUT

TRANSITION/TRANSVERSION STATISTICS

--TsTv

Calculates the Transition /

Transversion ratio in bins of size defined by this option.

Only uses bi-allelic SNPs. The resulting output file has the

suffix ".TsTv".

--TsTv-summary

Calculates a simple summary of

all Transitions and Transversions. The output file has the

suffix ".TsTv.summary".

--TsTv-by-count

Calculates the Transition /

Transversion ratio as a function of alternative allele

count. Only uses bi-allelic SNPs. The resulting output file

has the suffix ".TsTv.count".

--TsTv-by-qual

Calculates the Transition /

Transversion ratio as a function of SNP quality threshold.

Only uses bi-allelic SNPs. The resulting output file has the

suffix ".TsTv.qual".

--FILTER-summary

Generates a summary of the

number of SNPs and Ts/Tv ratio for each FILTER category. The

output file has the suffix ".FILTER.summary".

OUTPUT

NUCLEOTIDE DIVERGENCE STATISTICS

--site-pi

Measures nucleotide divergency

on a per-site basis. The output file has the suffix

".sites.pi".

--window-pi

--window-pi-step <integer>

Measures the nucleotide

diversity in windows, with the number provided as the window

size. The output file has the suffix

".windowed.pi". The latter is an optional argument

used to specify the step size in between windows.

OUTPUT FST

STATISTICS

--weir-fst-pop

This option is used to

calculate an Fst estimate from Weir and Cockerham’s

1984 paper. This is the preferred calculation of Fst. The

provided file must contain a list of individuals (one

individual per line) from the VCF file that correspond to

one population. This option can be used multiple times to

calculate Fst for more than two populations. These files

will also be included as "--keep" options. By

default, calculations are done on a per-site basis. The

output file has the suffix ".weir.fst".

--fst-window-size

--fst-window-step <integer>

These options can be used with

"--weir-fst-pop" to do the Fst calculations on a

windowed basis instead of a per-site basis. These arguments

specify the desired window size and the desired step size

between windows.

OUTPUT OTHER

STATISTICS

--het

Calculates a measure of

heterozygosity on a per-individual basis. Specfically, the

inbreeding coefficient, F, is estimated for each individual

using a method of moments. The resulting file has the suffix

".het".

--hardy

Reports a p-value for each site

from a Hardy-Weinberg Equilibrium test (as defined by

Wigginton, Cutler and Abecasis (2005)). The resulting file

(with suffix ".hwe") also contains the Observed

numbers of Homozygotes and Heterozygotes and the

corresponding Expected numbers under HWE.

--TajimaD

Outputs Tajima’s D

statistic in bins with size of the specified number. The

output file has the suffix ".Tajima.D".

--indv-freq-burden

This option calculates the

number of variants within each individual of a specific

frequency. The resulting file has the suffix

".ifreqburden".

--LROH

This option will identify and

output Long Runs of Homozygosity. The output file has the

suffix ".LROH". This function is experimental, and

will use a lot of memory if applied to large datasets.

--relatedness

This option is used to

calculate and output a relatedness statistic based on the

method of Yang et al, Nature Genetics 2010

(doi:10.1038/ng.608). Specifically, calculate the unadjusted

Ajk statistic. Expectation of Ajk is zero for individuals

within a populations, and one for an individual with

themselves. The output file has the suffix

".relatedness".

--relatedness2

This option is used to

calculate and output a relatedness statistic based on the

method of Manichaikul et al., BIOINFORMATICS 2010

(doi:10.1093/bioinformatics/btq559). The output file has the

suffix ".relatedness2".

--site-quality

Generates a file containing the

per-site SNP quality, as found in the QUAL column of the VCF

file. This file has the suffix ".lqual".

--missing-indv

Generates a file reporting the

missingness on a per-individual basis. The file has the

suffix ".imiss".

--missing-site

Generates a file reporting the

missingness on a per-site basis. The file has the suffix

".lmiss".

--SNPdensity

Calculates the number and

density of SNPs in bins of size defined by this option. The

resulting output file has the suffix

".snpden".

--kept-sites

Creates a file listing all

sites that have been kept after filtering. The file has the

suffix ".kept.sites".

--removed-sites

Creates a file listing all

sites that have been removed after filtering. The file has

the suffix ".removed.sites".

--singletons

This option will generate a

file detailing the location of singletons, and the

individual they occur in. The file reports both true

singletons, and private doubletons (i.e. SNPs where the

minor allele only occurs in a single individual and that

individual is homozygotic for that allele). The output file

has the suffix ".singletons".

--hist-indel-len

This option will generate a

histogram file of the length of all indels (including SNPs).

It shows both the count and the percentage of all indels for

indel lengths that occur at least once in the input file.

SNPs are considered indels with length zero. The output file

has the suffix ".indel.hist".

--hapcount

This option will output the

number of unique haplotypes within user specified bins, as

defined by the BED file. The output file has the suffix

".hapcount".

--mendel

This option is use to report

mendel errors identified in trios. The command requires a

PLINK-style PED file, with the first four columns specifying

a family ID, the child ID, the father ID, and the mother ID.

The output of this command has the suffix

".mendel".

--extract-FORMAT-info

Extract information from the

genotype fields in the VCF file relating to a specfied

FORMAT identifier. The resulting output file has the suffix

".<FORMAT_ID>.FORMAT". For example, the

following command would extract the all of the GT (i.e.

Genotype) entries:

vcftools --vcf file1.vcf

--extract-FORMAT-info GT

--get-INFO

This option is used to extract

information from the INFO field in the VCF file. The

<string> argument specifies the INFO tag to be

extracted, and the option can be used multiple times in

order to extract multiple INFO entries. The resulting file,

with suffix ".INFO", contains the required INFO

information in a tab-separated table. For example, to

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