VCF files for Indels and SNPs
I am following the Best Practices for DNAseq analysis and have 2 quick questions:
1. I wanted to confirm if the VCF files produced after the VariantRecalibrator and ApplyRecalibration steps for SNP and for Indels are completely independent of each other. In other words, the VCF file produced after these two steps for SNPs (mode SNP) is just for SNPs and for Indels (mode INDEL) is just for Indels.
2. What is the source of the ALT alleles in the VCF file - is it the various annotation files that were used during the analysis?