BEDgraph to BED/bam

Question

[wanziyi89]

Hi guys,

Any tools or software available for converting bedgraph to bed and then to bam?

I would like to extract CpG methylation calls using bismark and then save them in Bam format then convert them to bam using bedtools.

I saw some references to manually convert bedgraph to bed via UNIX commands, just wondering is there any tools to directly do the job?

[Devon Ryan]

It's not clear how one would store the information in a bedGraph file as a BAM file. Certainly the interval is trivial to encode, but BAM files aren't intended to convey arbitrary decimal scores like bedGraph. Why not use a bigWig file instead? It's binary like BAM files and can be loaded similarly in genome viewers and has the benefit that it's actually intended to hold information like this.