Need help converting vcf files to snp
1
0
Entering edit mode
@de4bb89e
Last seen 7 weeks ago
United States

I have no knowledge of anything related to this topic. I received my raw data files from my geneticist but they are in vcf format and the sites im trying to upload too only accept snp or indel files. They vcf files I have are too large to upload. I looked into snps python but am clueless on what to do.

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
VCFArray • 477 views
ADD COMMENT
0
Entering edit mode

You can search the Bioconductor list of software for vcf and have a few packages that may be useful. If you click on the package it will take you to their landing page where you can find package vignettes/manuals/documented functions. https://bioconductor.org/packages/release/BiocViews.html#___Software See alabaster.vcf, TVTB, fastreeR, VCFArray, and VariantExperiment

ADD REPLY
0
Entering edit mode
@james-w-macdonald-5106
Last seen 46 minutes ago
United States

There is not, to my knowledge, a file format called 'snp', nor 'indel'. Perhaps you could provide the link to the site you are trying to upload to?

0
Entering edit mode

This is the link to the website I was trying to upload it to. Any other website denies my files saying it is the incorrect format. https://genvue.geneticgenie.org/

ADD REPLY
0
Entering edit mode

That website specifically calls for VCF files, which is what you say you have.

ADD REPLY
0
Entering edit mode

it also mentions the files cannot be larger than 1gb. my files arew between 3-5 gb.

ADD REPLY

Login before adding your answer.

Traffic: 786 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6