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Old 06-27-2012, 02:43 AM   #1
zun
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Default drosophila indel database(for GATK purpose)

Hello there,

I am looking for the database for Drosophila indels.

I tried to use GATK's snv calling tool, but it requires known indel vcf file to implement realignment around known indels.

I found out there are two indel databases for human and rice, but not for drosophila....

Do anyone know such database? or when using GATK, which reference vcf file do you use? or do you make it by yourself?

any help would be appreciated!

zun
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Old 06-27-2012, 04:43 AM   #2
adaptivegenome
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You do not need a known indel list to do GATK realignment. TargetCreator can make a list for your genome based on indels and SNP clusters in your genome. However we are working on an indel list for Drosophila based a population of 205 lines. I can share more details if you send me a PM.

Last edited by adaptivegenome; 06-27-2012 at 04:46 AM. Reason: Typo
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Old 06-27-2012, 05:23 PM   #3
zun
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>genericforms

thank you for your reply!

oh, it seems I misunderstood GATK's realingment...

Actually, what I want to do is to compare the accuracy amang SNV calling tools, and in the end to build pipelines for wg/exosome analysis.
I chose Drosophila genome as it is small and I thought it would not take much time to finish whole pipeline(mapping,duplication removal, SNP calling...).

I used dwgsim to create random paired-end reads from Drosophila Release 5 genome seaqunce downloaded from BDGP site.
Mapping by bwa, then GATK/samtools pileup/other tools for realignment, SNV callings.

If its impossible/difficult to get drosophila known indels, I was thinking to use one of human chromosomes for test.

ok i will send you a pm later!

zun
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Old 06-27-2012, 06:44 PM   #4
adaptivegenome
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If you have no interest in flies and simply want to work with a small dataset I definitely recommend using a human chromosome. I think it is a better approximation of the human genome than using the fly genome.
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Old 06-27-2012, 06:58 PM   #5
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ok sure, will use a human chromosome!
thank you for your time :-)

zun
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Old 06-27-2012, 07:14 PM   #6
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Good luck!
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