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Bioinformatics Validation 'whole Exome variant calling pipeline' following GIAB data set 'NA127878'

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Dear Esraa, 
i hope you are doing well 
i am working on Exome pipeline validation using NA12878 and GIAB data set, i designed the pipeline base on BWA and Samtools and i got my VCF file, i did compare it with GIAB VCF file but i'm not sure if i did it in the right way and i did not get the result that i wish. 
i need you consultation on this matter and it will helps if we arrange an online meeting 'ex:Zoom' to explains to you what i did and answer any question you have before starting the project
project Budget and Duration will be decided later 
Thank you !
Abdullah