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Genotype depth filters: SNPs DP>10 and Indels DP>10 for indels.
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.
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
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This implements some recommendations from UK Biobank on exome sequence data quality control.
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
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