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KGGSeq

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

KGGSeq is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits.Simply, KGGSeq is like a fishing rod facilitating geneticists to fish the genetic determinants of human diseases/traits in the big sea of DNA sequences. Compared with other genetic tools like plink/seq, KGGSeq paid more attention downstream analysis of genetic mapping. Currently, a comprehensive and efficient framework was newly implemented on KGGSeq to filter and prioritize genetic variants from whole exome sequencing data.
For further information, see the online documentation of KGGSeq.

Options

KGGSeq Jar
Set the path to the KGGSeq Jar File.
VCF Input
Set the path to the input VCF File.
PED Input File
Set the path to the PED pedigree file containing the description of the individuals relationships.
Local path to the resource datasets
Set the path to resource datasets.
General Options
Build Version: Specify the database and reference genome version.
Composite Subject ID: By checking this option KGGSeq uses a composite subject ID in the VCF file.
Output Prefix: Define a prefix for all output files of this run.
Output Format: Choose either excel or csv as output format.
Quality Cutoffs
Seq Qual: Set the minimum overall sequencing quality score (Phred Quality Score) for the variant at x. (Default setting = 50.0)
Seq MQ: Set the minimum overall mapping quality score (Phred Quality Score) for the variant at x. (Default setting = 20)
Seq SB: Set the maximal overall strand bias score for the variant at x. (Default setting = -10.0)
Gty Qual: Exclude genotypes with the minimal genotyping quality (Phred Quality Score) per genotype < x. (Default setting = 20)
Gty DP: Exclude genotypes with the minimal read depth per genotype < x. (Default setting = 8)
Gty Sec Pl: Exclude genotypes with the second smallest normalized, Phred-scaled likelihoods for genotypes < x. (Default Setting = 20)
Gty Af Ref: Exclude genotypes with the fraction of the reads carrying alternative allele > = x% at a reference-allele homozygous genotype. (Default value = 0.05)
Gty Af Het: Exclude genotypes with the fraction of the reads carrying alternative allele < = x% at a heterozygous genotype. (Default value = 0.25)
Gty Af Alt: Exclude variants with the fraction of the reads carrying alternative allele < = x% at a alternative-allele homozygous genotype. (Default value = 0.75)
Annotation Options
For detailed explanations, see online KGGSeq user manual.
Genotype Filter: Filter out variants for which their genotypes are not consistent with the assumption of disease inheritance pattern (4=Exclude variants at which both affected and unaffected subjects have the same heterozygous genotypes). For complete list see online KGGSeq user manual.
Ignore Homo: Ignore homozygous mutations
Select Gene Features: Select variants by specific features: Frameshift(1), Nonframeshift(2), Startloss(3), Stopgain(4), Splicing(5), Missense(6), ...Unknown(17). For complete list see online KGGSeq user manual.
Filter by Common variants: Specify databases which are used for allele frequency filtration.
Prioritize sequence variants by disease-causing prediction: Uses dbNSFP v3.0+ database to RE-predict whether a nonsynonymous single nucleotide variant (SNV) will potentially be Mendelian disease causal or not.
Prioritize sequence variants by other genomic and OMIM annotation: KGGSeq can extract all available disorder names linked to a gene in which the variants are located from the OMIM dataset morbidmap
Prioritize sequence variants by PubMed: KGGSeq can mine the titles and abstracts of published papers in PubMed via the NCBI E-utilities to find a co-mention with the searched term(s) of interest.
Prioritize sequence variants by candidate genes with protein interaction information: Examine whether variants share the same PPIs with candidate genes. In this case, a file including the candidate gene names has to be specified.
Prioritize sequence variants by candidate genes with pathway information: Examine whether variants share the same genesets with candidate genes. In this case, a file including the candidate gene names has to be specified.

Input Ports

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No description for this port available.

Output Ports

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Currently returns inData

Views

STDOUT / STDERR
The node offers a direct view of its standard out and the standard error of the tool.

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Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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