I am working on cattle genomics and now, I am looking for a validated cattle SNPs used for VQSR approach in GTAK. Is there any validated cattle SNPs? If not, am I suppose to use a separate vcf or combined (i.e. Includes SNP and INDELs) file for SNPs and INDELs Hard filtering?
1000 Bull Genomes Project aimed to sequence the genomes of a large number of cattle from various breeds and populations. The project provides a database of genetic variants, including validated SNPs, which you can access to find relevant variants for your study.
Regarding the VCF (Variant Call Format) file for SNP and INDEL hard filtering, the recommended approach is to use separate VCF files for SNPs and INDELs. This separation allows you to apply different filtering criteria specific to each variant type. GATK provides separate tools and parameters for hard filtering SNPs and INDELs, such as VariantFiltration and SelectVariants. By using separate VCF files, you can tailor the filtering parameters to the specific characteristics of each variant type and achieve better control over the filtering process.
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