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Hi, I am new to WGS and would like to know how the genotype is attributed. It seems it does not depend much on depth of allele ratio. We ran GATK3.6 and Freebayes on the same BAM files and intersected them for genotype differences between monozygotic twins. We got stuck selecting among 16k variants, not knowing which filtering to apply. GATK has much better concordance between allele ratio and genotype than Freebayes giving higher coverage. Two questions: (1) is there any relationship between coverage (individual allele depth) and genotype? (2) What is the best practice (strategy) to filter out variants from WGS after intersecting 2 pipelines??? Thank you -Anne