Regarding vcf to bed

Question

[DL]

Hello everyone,

Can any one tell me that how can i convert vcf to bed ?? i coverted it using vcf2bed and the command is ==>

vcf2bed   < DK_results_snps.vcf >DK_snp.bed

but when i count number of snp in bed file and snp from vcf file then its different in number. i even removed the # tag from bed file and then use

wc -l dk_snp.bed

while for vcf file, i used bcftools. Please tell me how can i convert it?? Thanks in advance Deepika

Answer 1

[Pierre Lindenbaum]

http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html

If the ALT field contains more than one allele, multiple BED records will be printed.

[DL]

Thank you for your quick response. So, in summary of analysis, i should count number of snps from vcf file or from the bed file ??