Question

GUI for VCF filtration

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4.5 years ago

Manuel ▴ 410

Hi,

what would be good tool choices for filtering VCF files graphically (IOW: usable for a biologist/clinician)? Does any handle smallish cohorts of unrelated invidiuals?

Thanks,

vcf variant filtration • 957 views

ADD COMMENT • link 4.5 years ago by Manuel ▴ 410

score 1 · Answer 1 · 2019-10-29

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4.5 years ago

JC 13k

Qiagen IVA is nice (not free)

ADD COMMENT • link 4.5 years ago by JC 13k

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I think you meant to point to Ingenuity Variant Analysis (IVA) which is a different tool. There is also VarSeq and SN/Variation Suite from DNAHelix. Neither are free.

ADD REPLY • link 4.5 years ago by GenoMax 141k

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Thanks, that is the one.

ADD REPLY • link 4.5 years ago by JC 13k

score 1 · Answer 2 · 2019-10-29

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4.5 years ago

Pierre Lindenbaum 161k

see:

CuteVariant : A GUI to filter VCF file
GUI filtering annotated vcf
opensource grafical user interface for filtering millions of annotated variant
User Friendly VCF Filtering Tools
galaxy
I also wrote https://www.biorxiv.org/content/10.1101/120196v1 but it requires java jfx.

ADD COMMENT • link 4.5 years ago by Pierre Lindenbaum 161k