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Old 01-28-2011, 02:13 AM   #1
ketan_bnf
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Location: India

Join Date: Oct 2010
Posts: 59
Default Converter for vcf to bed format

Hi all,

Is there any converter that can convert vcf format files obtained by samtools vcfutils.pl to bed format?

Because i want predict the variant effect using varian_effect_predictor of ensemble.

##fileformat=VCFv4.0
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GKUNU9Q04_chr1_sort.bam
chr1 46707 . A G 7.59 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=60 PL:GT:GQ 38,6,0:1/1:49
chr1 168576 . C T 4.61 . DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=60 PL:GT:GQ 34,6,0:1/1:49
chr1 168635 . G A 17.1 . DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=60 PL:GT:GQ 49,9,0:1/1:63

To

1 46707 46707 A/G +
1 168576 168576 C/T +
1 168635 168635 G/A +
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