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Old 08-26-2013, 08:52 AM   #1
id0
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Default D. melanogaster known SNPs and indels

I am working with the fly genome for the first time. I am trying to do realignment and recalibration, which requires known SNPs. Where can I find these (preferably for the UCSC dm3 genome)?

I found FlySNP (http://flysnp.imp.ac.at/). That seems to be what I am looking for. However, the genome version is not specified and there seems to be no easy way to export the data.

UCSC does not provide any SNP tracks for the fly like it does for human or mouse, which makes me a little concerned that there is no reliable resource.

Any insights from someone with D. melanogaster experience would be greatly appreciated.

Last edited by id0; 08-26-2013 at 08:55 AM.
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Old 08-26-2013, 11:08 AM   #2
aaronh
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Here are the VCF files from the DGRP: http://www.hgsc.bcm.tmc.edu/projects...013/vcf_files/
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Old 08-26-2013, 11:46 AM   #3
id0
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Quote:
Originally Posted by aaronh View Post
Here are the VCF files from the DGRP: http://www.hgsc.bcm.tmc.edu/projects...013/vcf_files/
That looks great!

Which genome version is that? I couldn't find that info on the DGRP website.
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Old 08-26-2013, 11:52 AM   #4
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It is either flybase 5.something or dm3. They are the same thing, just with or without the leading chr.
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Old 08-26-2013, 12:19 PM   #5
id0
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Quote:
Originally Posted by aaronh View Post
It is either flybase 5.something or dm3. They are the same thing, just with or without the leading chr.
I saw that the positions are without the leading "chr", so that did not look like dm3. Thanks for clarifying that the actual coordinates should be identical.
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Old 08-26-2013, 12:19 PM   #6
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I've worked extensively with the DGRP and can find out which reference was used if it's vital information. My understanding, however, is that most of the revisions of the reference have been annotation and not modifications to the sequence (though I've only heard this - never checked myself).
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Old 08-26-2013, 12:25 PM   #7
id0
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Quote:
Originally Posted by spvensko View Post
I've worked extensively with the DGRP and can find out which reference was used if it's vital information. My understanding, however, is that most of the revisions of the reference have been annotation and not modifications to the sequence (though I've only heard this - never checked myself).
I assume the sequence is stable by now as this is a common organism, genome is fairly small and has not been updated in a while. However, I have no experience with the fly genome, so I am not sure if there are any caveats.

I am trying to do recalibration, so it's fairly important that the positions are accurate.
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