VCF data QC default setting

[gaow]

This implements some recommendations from UK Biobank on exome sequence data quality control.

1. Genotype depth filters: SNPs DP>10 and Indels DP>10 for indels.
2. At least one sample per site passed the allele balance threshold >= 0.15 for SNPs and >=0.20 for indels (heterozygous variants).
   • Allele balance is calculated for heterozygotes as the number of bases supporting the least-represented allele over the total number of base observations.
3. Genotype quality GQ>20

Additionally, variant level missing data 10% and HWE 1E-6 are also applied, similar to GWAS QC using PLINK.

TS/TV ratio are computed in the pipeline for known variants vs novel variants (annotated by dbSNP database which is also part of the pipeline). Users are encouraged to review these before/after QC