Converting Dindel VCF file to GATK BED file

MolecularToast · 12-08-2010, 07:53 PM

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,

adrian · 12-13-2010, 04:34 PM

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

how could this be done?

thanks

BetterPrimate · 09-24-2011, 07:38 PM

Read the required file format on Seattleseq here:
http://gvs.gs.washington.edu/Seattle...sp#FILE-FORMAT

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12-08-2010, 07:53 PM	#1
MolecularToast Junior Member Location: Iowa Join Date: Aug 2010 Posts: 9	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,

12-13-2010, 04:34 PM	#2
adrian Member Location: baltimore Join Date: Oct 2009 Posts: 89	hello: did you solve the problem of converting dindel VCF to GATK bed file? how could this be done? thanks

09-24-2011, 07:38 PM	#3
BetterPrimate Member Location: NSW Join Date: May 2010 Posts: 15	Read the required file format on Seattleseq here: http://gvs.gs.washington.edu/Seattle...sp#FILE-FORMAT