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Old 04-18-2011, 09:49 AM   #1
newbietonextgen
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Location: USA

Join Date: Nov 2010
Posts: 56
Default Calling multiple BAM files for SNPs and vcf

Hi all,

I am in the process of calling SNPs using GATK. I do know that the unifiedgenotyper will call from multiple BAM files. The question is about the resulting VCF file.
1) Does the VCF file separate out the SNps? In other words, will i know which BAM sample file contributed to what SNP in the VCF file? In such as way i could just parse back individual sample SNPs back, if needed.
2) Also it it better to call SNPs from individual files or pool all the BAM files from the same treatment to get better depth?

The BAMs have unique Read Groups. Any help will a appreciated.

Thanks

Last edited by newbietonextgen; 04-18-2011 at 10:51 AM.
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