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Forum: Bioinformatics 02-20-2012, 08:22 AM
Replies: 0
Views: 849
Posted By LauraSmith
Post convention of representing alleles in a BED file

Does anyone know what is the convention of representing alleles in a BED file. For a given genomic coordinate, should the alleles be always represented according to positive strand? (even if we are...
Forum: Bioinformatics 02-17-2012, 12:47 PM
Replies: 0
Views: 1,412
Posted By LauraSmith
Post How to represent reference and observed alleles in BED files for variants on negative

Hi Everyone,

I have a question about the BED detail format described on the UCSC browser webpage. http://genome.ucsc.edu/FAQ/FAQformat#format1

There is an example there as the following:...
Forum: Bioinformatics 02-15-2012, 09:35 AM
Replies: 3
Views: 7,260
Posted By LauraSmith
Post Is there a BED file format validator? Does a BED file have to be sorted position?

Hi Everyone,

I have 2 questions and would very much appreciate anyone's input:

1. Is there a BED file format validator? A tool or a java package perhaps available online to download?


2....
Forum: Bioinformatics 12-05-2011, 08:51 AM
Replies: 4
Views: 8,144
Posted By LauraSmith
Post Is there a tool that converts TXT, BED, GFF format to VCF?

Hi,

I would like to ask if there is tool out there that would convert variants in a certain file format (such as .txt, .gff, .bed) to VCF format?

Thank you for your help.
Laura
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