BEDtools merge output

Question

[tea.vuki]

Hello, bedtools merge can take several input types: <BED/GFF/VCF/BAM> , my question is whether output is always in BED format? For example if I run the command bedtools merge -i example.vcf, output will be in BED format and not VCF format?

Thanks in advance!

[jv]

If you are concerned about the applicability of bedtools merge to VCF files, consider using bcftools instead: https://samtools.github.io/bcftools/bcftools.html

Answer 1

[raphael.B]

Hello, Bedtools merge returns bed files, even with VCF input.

Answer 2

[ahmad mousavi]

try merge command in VCFtools , also there many many others tools in the net.