creating BAM? alignment files for IGV

Question

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Hi, I have coordinate data for several sequences I want to align against genomes in IGV. The preferred format for alignment is said to be BAM. Unfortunately I haven't found a straightforward way of creating BAMs straight from coordinates. I assume I'll need the reference genome as well. Is there any simple way to do it from R/Bioconductor?

[h.mon]

Do you have sequences you want to align, or do you have sequences (whose coordinates you know already) which you to display? If you have the genomic coordinates, all you need is a tab-delimited .BED file with:

chromName     gene1StartPos      gene1EndPos
chromName     gene2StartPos      gene2EndPos
...

And yes, to display on IGV you do need the reference genome.