Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 12:31 AM
IUPAC coded reference sequences data Bioinformatics 9 11-29-2011 07:50 PM
how to create junctions file based off reference zorph Bioinformatics 0 11-08-2011 08:42 AM
How to create a GRangesList object for genome not from UCSC? dicty Bioinformatics 2 02-16-2011 06:51 AM
Reference genome for MAQ - split reference genome by chromosome or not? inesdesantiago Bioinformatics 4 02-18-2009 08:44 AM

Thread Tools
Old 08-21-2012, 06:42 AM   #1
Junior Member
Location: Columbus, OH

Join Date: Dec 2010
Posts: 1
Default looking to create IUPAC reference genome

I am looking for a way to replace the reference allele within a reference genome with the IUPAC code for SNPs of my choosing.

I have been using the FastaAlternateReferenceMaker from GATK to simply switch the reference for the variant allele; however, the application gives an error when I try to switch the allele to a non-nucleotide letter.

amythecat is offline   Reply With Quote
Old 06-12-2013, 11:42 PM   #2
Junior Member
Location: Thailand

Join Date: Jun 2013
Posts: 3

Did you ever find an answer to this?
bmuchmore is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:16 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO