Category
Format Conversion
Usage
bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome>
Manual
Required arguments
- -i <bed/gff/vcf>: Input bed file
- -g <genome>: genome’s chrom sizes. This can be retrieved with tools like
fetchChromSizes
Options
- -mapq INT: Set the mappinq quality for the BAM records. Default: 255
- -bed12: The BED file is in BED12 format. The BAM CIGAR string will reflect BED "blocks".
- -ubam: Write uncompressed BAM output. Default writes compressed BAM.
Notes
bedtools bedtobam is also known as bedToBam- BED files must be at least BED4 to create BAM (needs name field).
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