Test-drive the GATK tools and Best Practices pipelines on Terra
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1000Genome reference gvcf files for GenotypeGVCF
I am using GATK 2014.3-3.2.2-7-gf9cba99. I use GenotypeGVCF tool for joint genotying of my samples, where I consider 1000Genome reference gvcf files along with all the gvcf files of the batch. I observe that after this step when I split individual sample.vcf files there are more number of variants (1328 in my sample). But the same sample variants, after vqsr filteration, has 230 variants.
I ran the GenotypeGVCF step of the same batch of samples (gvcf files) without 1000Genome reference gvcf files. Then I got the same sample.vcf file with 419 variants after the spliting. The same file, after vqsr filteration, has 268 variants. My question is,
1)What is the impact of 1000Genome gvcf files in Joint genotyping?
2)Why the variant number is reduced after vqsr filteration, in the case where 1000Genome gvcf files were considered for joint genotyping?
Thanks in advance,