VCF to pseudo BAM

[dagarfield]

I've an odd question.
I'm working with a set of VCF files from multiple individuals in a population. However, there are a number of tools for population genetic analyses (e.g. popbam) that take BAM files as inputs. I don't suppose anyone has a tool for converting a VCF file into a pseudo-BAM file (e.g. a set of arbitrarily long reads against the reference genome), do they? I admit, this would obviously be a rather silly looking BAM file....however, it would get the job done.

Alternatively, anyone have a nice pop gen toolkit for VCF files? It looks like the next release of vcftools will have some nice additions along these lines, but it is hard to find much out there that calculates more than pi and, sometimes, Tajima's D.

Thanks.

[hl450]

Have you had any success converting VCF to pseudo BAM? I would love to find out if there is any tools out there. Thanks.

[dagarfield]

In the end, I went with a hybrid approach of writing a few scripts of my own plus one that translates a vcf to a phylip (or hapmap) file so that the data can be processed by VariScan. In truth this is probably more efficient than converting to BAM format for the sake of using popBam (which is good, but has a few limitations of its own).

My scripts were built fairly specifically for inbred lines, but I'm happy to pass them along if you like.

[chofman]

I would love to try your script that converts vcf to phylip! I've been struggling to do that myself.