Post filtering analysis for exome data

Question

[priya.bmg]

Hello

I am following GATK pipeline to process exome data set. I am done with preprocessing step and filtered the dataset by hard filtering method. Now, I am looking for variants shared between the affected individuals. In the vcf file, I get the variant allele position and genotype in the affected individuals. For example, variant is G allele and reference allele is C, genotype is given as CC in individual 1, CG in individual 2, GG in individual 3 and CG in individual 4. So, here except individual 1, all the individuals share the variant allele. This is how I have to look for shared variants between affected individuals?.

After the hard filtering step, I should retain the variants that has high quality score in the vcf for subsequent analysis?. The variants has the label PASS label and use for subsequent annotation analysis?. Please advice

Thanks

[Pierre Lindenbaum]

please, stop asking questions without validating the answers or commenting

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