The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
RAW VCF has a significantly higher amount of variations than the total of (RAW SNPS + RAW INDELS)
I successfully ran a variant calling pipeline and got the raw.vcf file obtained by haplotype caller which contains exactly 4,484,688 records. And then I processed it further by extracting SNPs and INDELs to seperate VCF files using SelectVariants , and it yielded a vcf for raw SNPs with 85,239 records and a vcf for raw INDELs with 14,501 records. As you can see there is a significant decrease of the total number of records. where almost 4 million records were ignored. Could you please explain me what's the process behind all these and why is this happening ?