BEDOPS convert2bed output
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Entering edit mode
7 weeks ago
nehaklkn • 0

I am trying to convert dbsnp v155 hg19 vcf data from NCBI to bed format. I have a subset of the vcf file as input to convert2bed. My observation is that the output BED file contains intervals which are 1bp in length even for certain indels that are more than 1bp in length. Can someone help me understand if convert2bed utility is to be used only for SNP's or can be used for other variations types as well?

for e.g. - input file - NC_000001.10 10129 rs1639546602 CCCTAA C . . RS=1639546602;dbSNPBuildID=155;SSR=0;PSEUDOGENEINFO=DDX11L1:100287102;VC=INDEL;R5;GNO;FREQ=GnomAD:1,1.353e-05

output of convert2bed - NC_000001.10 10128 10129 rs1639546602 . CCCTAA C . RS=1639546602;dbSNPBuildID=155;SSR=0;PSEUDOGENEINFO=DDX11L1:100287102;VC=INDEL;R5;GNO;FREQ=GnomAD:1,1.353e-05

RefSNP entry - rs1639546602

Reference SNP Report

vcf bedops convert2bed bed • 136 views
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