Author: Allison J Cox; Fillan Grady; Gabriel Velez; Vinit B Mahajan; Polly J Ferguson; Andrew Kitchen; Benjamin W Darbro; Alexander G Bassuk
Title: In trans variant calling reveals enrichment for compound heterozygous variants in genes involved in neuronal development and growth. Document date: 2018_12_13
ID: j5jrpbst_17
Snippet: Varcount is a free, open source tool useful for the quantification of heterozygous, homozygous, or compound heterozygous mutations per sample. Input variants may be phased or unphased. All python scripts and supporting files may be downloaded from Github at https://github.com/GeneSleuth/VarCount. Supporting files include the "parameters.txt" file where the user may select variant filters for mutation effect, minor allele frequency, and inheritanc.....
Document: Varcount is a free, open source tool useful for the quantification of heterozygous, homozygous, or compound heterozygous mutations per sample. Input variants may be phased or unphased. All python scripts and supporting files may be downloaded from Github at https://github.com/GeneSleuth/VarCount. Supporting files include the "parameters.txt" file where the user may select variant filters for mutation effect, minor allele frequency, and inheritance pattern (homozygous, compound heterozygous, one mutation or two mutations), and Sample filters based on information entered into the "SampleInfo file". Input vcf files must be annotated with SNPSift/SNPEff using the dbNSFP and GRCh37/38 databases. A readme file with instructions is also provided.
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