bam to bed

Question

[mahdi_sh1387]

hello my friends; I have a question: I have two sample .bam file from illumina for my patient, now I want to know if i convert this two file to bed file, does any different between two bed file?

thanks Mahdi

[Devon Ryan]

The program you use to make the BED files is unlike to discriminate between the samples according to read group, so I'd encourage you not to bother with this. Why do you want a BED file to begin with? I would think that you'd want a VCF file instead.

[ATpoint]

It is unclear what you want. Please post a representative output.