variant calling

kjaja · 11-04-2011, 07:15 AM

Are there tools out there that help in processing the variants calling output files from CASAVA? I have all the variant call files (SNPs and Indels) for all the individuals and I am looking into proceeding with analysis (case control study)

I appeciate your help

m_elena_bioinfo · 11-04-2011, 08:16 AM

Hi! You can use a lot of different pipeline and tools for the variant calling. As free software, you can use samtools or GATK, games and annovar in the final step for the annotation of the identified variants

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11-04-2011, 07:15 AM	#1
kjaja Member Location: NY Join Date: Aug 2011 Posts: 55	variant calling Are there tools out there that help in processing the variants calling output files from CASAVA? I have all the variant call files (SNPs and Indels) for all the individuals and I am looking into proceeding with analysis (case control study) I appeciate your help

11-04-2011, 08:16 AM	#2
m_elena_bioinfo Member Location: Ospedali Riuniti di Bergamo, ITALY Join Date: Oct 2009 Posts: 99	Hi! You can use a lot of different pipeline and tools for the variant calling. As free software, you can use samtools or GATK, games and annovar in the final step for the annotation of the identified variants