BEDTOOLS bedtobam question

[LacquerHead]

Hi all,

Quick question, did some shifting of a BAM file by first converting it into BED with bamtobed and shifting with an awk script, however when I converted it back to bam after the file size reduced by 1/3 from 750mb to 250mb. Although when I run samtools flagstat on both before and after it shows me 22 million reads in both the 750mb and 250mb files. Any ideas?

[Brian Bushnell]

I don't personally use the bed format, but the specification does not provide any fields for quality scores or bases. It's just for positions. So, even if it's possible to convert a bed file to a bam file, it will not be the original bam file, since bam -> bed is a lossy conversion. I'm not sure what will be in your bam file, but I don't expect it to contain bases, quality scores, cigar strings, or optional fields.

[WhatsOEver]

I'm even surprised that flagstat works on such a bam as you actually loose any information on flags (paired, orientation, alternative alignments, ...). And I also don't understand why you'd like to do something like bam->bed->bam?