SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK: sorting vcf file given a reference file jorge Bioinformatics 4 01-14-2015 12:16 PM
Is there a BED file format validator? Does a BED file have to be sorted position? LauraSmith Bioinformatics 3 05-21-2013 11:54 AM
Where can I get GM19240 HapMap cell line variant calls as VCF or a BED file adrian Bioinformatics 2 09-13-2012 01:27 AM
Dindel last stage error nothing in the var.VCF file pankajsvats Bioinformatics 3 02-02-2012 05:00 AM
Dindel VCF to GATK BED or other formats adrian Bioinformatics 0 12-13-2010 09:37 AM

Reply
 
Thread Tools
Old 12-08-2010, 06:53 PM   #1
MolecularToast
Junior Member
 
Location: Iowa

Join Date: Aug 2010
Posts: 9
Default Converting Dindel VCF file to GATK BED file

Does anyone have a script or know of one that is capable of converting the VCF file output of Dindel into the BED format output of the GATK's IndelGenotyper?

From this:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
9 10018192 0 GGA G 453 PASS DP=29;NF=0;NR=8;NRS=2;NFS=8;HP=2 GT:GQ 1/1:32
9 80919955 0 G GT 456 PASS DP=61;NF=0;NR=9;NRS=0;NFS=10;HP=1 GT:GQ 1/1:38

To this:

9 10018192 10018194 -GA:10/10
9 80919955 80919955 +T:12/13

The main reason I ask is that I'd like to use SeattleSeq to annotate my indel calls from Dindel but the only indel type format they accept right now is the GATK BED format.

Any thoughts?

Thanks,
MolecularToast is offline   Reply With Quote
Old 12-13-2010, 03:34 PM   #2
adrian
Member
 
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default

hello:
did you solve the problem of converting dindel VCF to GATK bed file?

how could this be done?

thanks
adrian is offline   Reply With Quote
Old 09-24-2011, 06:38 PM   #3
BetterPrimate
Member
 
Location: NSW

Join Date: May 2010
Posts: 15
Default

Read the required file format on Seattleseq here:
http://gvs.gs.washington.edu/Seattle...sp#FILE-FORMAT
BetterPrimate is offline   Reply With Quote
Reply

Tags
dindel, gatk

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 08:37 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO