Use of GenotypeGVCFs in population genetic studies
I have 16 whole genome sequenced samples from two populations (8 for each population). My goal is detection of signature of selection and introgression. I performed read cleaning, mapping to reference, mark duplication. SNP calling was performed using HaplotypeCaller in GATK for each sample separately.
Now my question:
For downstream analysis (PCA, ADMIXTURE analysis and detecting signature of selection), do I need to use GenotypeGVCFs command in GATK for genotype joining? Or I can create one VCF file per sample separately (without GenotypeGVCFs) and merge them for downstream analysis after variant filtering?
Thanks in advance
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