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I have use Unified Genotyper and Haplotype Caller from GATK to do the SNP calling from my RNA-seq data. Now, I have the .vcf files generated by these two tools and I need to process them. I have read documentations on Select Variant and Variant filteration, also the vcf tools but I am lost, I don't know what I should do first. I know there are lots of information out there on net but it would be great if you could give me some general outlines.
Thanks a lot in advance.