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This article mainly shows you "what are the basic parameters of vcftools", which is easy to understand and clear. I hope it can help you solve your doubts. Let me lead you to study and learn this article "what are the basic parameters of vcftools?"

Vcftools usage

Vcftools is a tool that can convert and filter VCF files and BCF files. We can use perl or python to write scripts to achieve many filtering and computing functions, but they are not as fast as this tool.

Basic parameters input parameters

-vcf supports v4.0, v4.1 or v4.2 VCF files

-gzvcf compressed VCF files via gzipped

-bcf BCF2 file

Output parameter

-out output file, followed by naming the output file directly

-stdout can take over the symbol to redirect the output

-temp specifies the output directory of the result

Filter parameters filter according to location

-chr

-not-chr

Include or exclude matching chromosome loci

-from-bp

-to-bp

These two parameters need to be used with-chr

Specify the lower and upper limits of a series of sites to be processed

-positions

-exclude-positions

Includes or excludes a set of sites based on the list of locations in the file. Each line of the input file should contain (tab delimited) chromosomes and locations

Filter by site

The name of the snp string can match the data of dbSNP and is suitable for the human genome. This instruction can be used many times.

-snps

-exclude

Include or exclude the SNP list given in the file

Variation type filtering

-keep-only-indels retains only indel tags

-remove-indels removes the indel tag

Filter based on flag

-remove-filtered-all Removes all sites with a FILTER flag other than PASS.

-keep-filtered

-remove-filtered

Filter based on INFO

-keep-INFO

-remove-INFO

Filter based on ALLELE

-maf MAF minimum filtering

-max-maf MAF maximum filtering

Many parameters are omitted here. For more information, please see the official website of vcftools.

Filter based on genotype value

-min-meanDP

-max-meanDP filters based on sequencing depth

-hwe

-max-missing integrity, which is between 0 and 1.

Filter according to material

-indv

-remove-indv

-keep

-remove

-max-indv

Genotypic filtering parameters

-remove-filtered-geno-all excludes that flag is not'.' And 'PASS'' genotypes

-remove-filtered-geno excluded flag as the genotype of string.

-minGQ excludes genotypes with GQ lower than this parameter.

-minDP

-maxDP

Calculation statistics accounting diversity statistics

-site-pi calculates all SNP

-window-pi

-window-pi-step

FST calculation

-weir-fst-pop

-fst-window-size

-fst-window-step

Other calculations

-het

-hardy

-site-quality is mainly used to extract the QUAL``` of each site in the VCF file.

-- missing-indv

-- missing-site calculates the deletion rate of each locus

Vcftools-vcf test.recode.vcf-missing-site-out ms

-SNPdensity calculates the density of SNP in the set bin

... It's too much. See the reference manual for details.

Output format

-recode

-recode-bcf

-recode-INFO

-recode-INFO-all

-contigs

Format conversion

-012

-IMPUTE

-ldhat

-ldhat-geno

-BEAGLE-GL

-BEAGLE-PL

-plink

Vcftools-vcf all.filter.vcf-plink-out aa

-plink-tped

-chrom-map

Comparison option

DIFF VCF FILE

-diff

-gzdiff

-diff-bcf

-diff-site

-diff-indv

-diff-site-discordance

-diff-indv-discordance

-diff-indv-map

-diff-discordance-matrix

-diff-switch-error

Example

1. Output the allele frequencies of all loci in the input vcf file from chromosome 1

Vcftools-gzvcf input_file.vcf.gz-freq-chr1-out chr1_analysis

two。 Outputs a new vcf file from the imported vcf file, which deletes any indel sites

Vcftools-vcf input_file.vcf-remove-indels-recode--recode-INFO-all-out SNPs_only

3. Output files compare sites in two vcf files

Vcftools-gzvcf input_file1.vcf.gz-gzdiff input_file2.vcf.gz-diff-site-out in1_v_in2

4. Export the new vcf file to standard output without any points with filter tags, and then use gzip to compress it

Vcftools-gzvcf input_file.vcf.gz-remove-filtered-all-recode-stdout | gzip-c > output_PASS_only.vcf.gz

5. Output Hardy-Weinberg p values for each site in the bcf file without any missing genotypes

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

6. Output nucleotide diversity in a series of locations

Zcat input_file.vcf.gz | vcftools-vcf-site-pi-positions SNP_list.txt-out nucleotide_diversity is all the contents of the article "what are the basic parameters of vcftools". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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