Variants in excel
I have inherited from a previous study a list of variants in excel. I do no have the original vcf files. What is the best way to analyze the variants in the excel file? I would like to use Varsifter or something similar but most packages seem to require vcf or vs formats. Thank you.
• 1,713 views
•
link
updated
by
colindaven
•
written
by
eleni.stylianou •
•
written
by
eleni.stylianou •
1 answer
Based on what I've seen, VCF files tend to be edited majorly by biologists so it might be you can't get them into VCF format again. As genomax says, even a limited VCF file format (i.e. with few INFO and or Genotype fields) might be highly beneficial.
Generally though, Excel is a data grave for all standard text formats.
• 0 views
•
link
written
by
colindaven
Log in to answer this question.
More posts like this
-
Rare Disease Variant Pathway Analysis
written by The_PyPanda •
-
Find ASVs for Non-Microbial Data
written by Saran •
-
Filter track list and variant list
written by Cong-Phuoc •
-
Is there a statistical way to estimate if a variant is de novo or inherited ? (In bacteria)
written by hugo.avila
-
Is there a way to force a specific order for variants in a PLINK file that have the same chromosome…
written by curious
-
Creating a set of rare variants shared by a child and a parents with VCF and Tabix
written by solene.conrad •
-
structural variant vcf file comparison
written by tarek.mohamed
-
Does vcftools or GATK have an option to skip indels when making alternate sequence?
written by severalorks
-
any tools for updating reference sequence file to include the variants from the vcf file?
written by mheyda •
-
Representative set for normal structural variation
written by dmyersturnbull •
Start with moving those out of excel into a standard delimited format file (perhaps they already are). Paste a sample of what you actually have so you can get useful answers.