This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there any specially designed software or a web service for the VCF file similarity search?

Is there any specially designed software or a web service for the VCF file similarity search, producing a report? Is there anything good beyond VCF compare commands in VCF, BCF tools, GATK?

vcf
• 972 views • link
written by genome21 • genome21

This question doesn't contain enough information. Please specify which input you have (and how many samples) and which would be the desired output.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Is there anything good beyond VCF compare commands in VCF, BCF tools, GATK?

what's wrong/missing with those tools ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hello genome21!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 0 views • link
written by Michael Dondrup Michael Dondrup

It depends on the reason you want to compare VCF files. What is the measure of similarity for you? In population analysis ADMIXTURE https://www.genetics.ucla.edu/software/admixture/ is one of the ways to cluster and then transform vcf files to vectors (called admixture vectors) and then compare these vectors. By admixture design vectors from within the same population will be closer.

If you want to find relatedness between two VCF samples you can look at the IBD with plink or use dedicated programs like KING to find kinship http://people.virginia.edu/~wc9c/KING/manual.html

Could you please specify your question?

• 0 views • link
written by Petr Ponomarenko Petr Ponomarenko

0 answers

No answers yet.

Log in to answer this question.

More posts like this