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VCF.Filter specifications

Information


Unique identifier OMICS_18440
Name VCF.Filter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data Lists of genetic variants, regions lists for filtering, cohort allele frequencies
Input format VCF
Output data Filtered genetics variants, Hilbert curve, Variants filtered on cohort allele frequencies
Output format VCF
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Heiko Muller
  • person_outline Christoph Bock

Publication for VCF.Filter

VCF.Filter citations

 (8)
call_split

An efficient pipeline to generate data for studies in plastid population genomics and phylogeography1

2017
Appl Plant Sci
PMCID: 5703179
PMID: 29188144
DOI: 10.3732/apps.1700053
call_split See protocol

[…] ), but in later rounds of haplotype estimation, A expands to contain estimated novel haplotypes in addition to the initial haplotypes. All instances of bi are read from the Pools file produced by the VCF filter.In each round of haplotype estimation, several values of A (each containing a different estimated haplotype) are tested. When creating new haplotypes, a SNP is only considered if there exis […]

call_split

ReliableGenome: annotation of genomic regions with high/low variant calling concordance

2016
Bioinformatics
PMCID: 5903559
PMID: 27605105
DOI: 10.1093/bioinformatics/btw587
call_split See protocol

[…] n we compare all called genotypes (in the VCF GT field) and write a merged variant call to a new joined VCF file Ji. A merged call is written as being ‘discordant’ (by using a respective entry in the VCF FILTER field) if the called genotypes did not match or if some call sets Ci,j did not contain a variant at this position. Otherwise it is written as being ‘concordant’ (using a ‘PASS’ filter). As […]

library_books

Methylation quantitative trait loci in the developing brain and their enrichment in schizophrenia associated genomic regions

2015
Nat Neurosci
PMCID: 4714325
PMID: 26619357
DOI: 10.1038/nn.4182

[…] ). Imputed genotypes were then filtered and recoded with PLINK1.9 removing samples with >5% missing values, and SNPs with >2 alleles, those indicated as a fail in the FILTER columns using the flag ‘--vcf-filter’, in addition to those characterized by >1% missing values, a Hardy-Weinberg equilibrium P < 0.001, a minor allele frequency of < 5%, or < 5 observations for any genotype group in line with […]

library_books

Large Scale SNP Discovery through RNA Sequencing and SNP Genotyping by Targeted Enrichment Sequencing in Cassava (Manihot esculenta Crantz)

2014
PLoS One
PMCID: 4281258
PMID: 25551642
DOI: 10.1371/journal.pone.0116028

[…] call format (VCF) file . Default parameters were used for GATK, which assumed a heterozygosity rate of one every 1000 bp. Variant calls with a quality less than 20 were subsequently removed with the VCF filter. […]

library_books

Genomic Evolution of the Pathogenic Wolbachia Strain, wMelPop

2013
Genome Biol Evol
PMCID: 3845649
PMID: 24190075
DOI: 10.1093/gbe/evt169

[…] n reads mapping to more than one location). Variants were called by first running nesoni freebayes with parameters −−depth-limit 220 and −−ploidy 4 and then reducing the ploidy to 1 by running nesoni vcf-filter on the VCF file produced by Freebayes.Variants identified in one strain were also checked in all other strains, both bioinformatically (using the pipelines above and via manual inspection o […]

library_books

ISPD gene mutations are a common cause of congenital and limb girdle muscular dystrophies

2013
PMCID: 3562076
PMID: 23288328
DOI: 10.1093/brain/aws312

[…] filter), including an indel mask consisting of 1000 Genomes pilot indels. Variants were assigned to quality tranches by GATK. The variants called by each of the callers were filtered separately using vcf-filter. For each sample, the resulting gatk.vcf and mpileup.vcf files were merged using vcf-isec. GATK annotations are preferred if sites are in both call sets. The variant calls were annotated us […]

Citations

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VCF.Filter institution(s)
Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; Fondazione Istituto Italiano di Tecnologia, Genoa, Italy; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St. Anna Kinderspital and Children’s Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; Max Planck Institute for Informatics, Saarbrucken, Germany
VCF.Filter funding source(s)
Supported by Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases; Austrian Academy of Sciences New Frontiers Group Award; ERC Starting Grant (European Union’s Horizon 2020 research and innovation programme) [679146 and 310857].

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