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Old 12-22-2016, 12:44 PM   #1
Location: New York

Join Date: Nov 2015
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Default BEDTOOLS bedtobam question

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?
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Old 12-22-2016, 03:42 PM   #2
Brian Bushnell
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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.
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Old 12-22-2016, 11:30 PM   #3
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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?
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