Effective filtering strategies to improve data quality from population-based whole exome sequencing studies

BMC Bioinformatics

Table 4 Splitting samples by batch (“batched”) retains more high quality variants

	HWE^*	Call rate^†	Ave.GQ^‡	VQSR^¥	Total
Number of variants filtered from “unbatched” dataset	14,209	197,540	0	26,967	238,716
Number of filtered variants found in “batched”	1,983	135,031	N/A	2,050	139,064
Ti/Tv of filtered variants found in “batched”	2.64	2.20	N/A	2.16	2.20

^*Used – hwe in vcftools to remove variants with Bonferroni-corrected p-value < 0.05.
^†Used – geno in vcftools to remove variants with call rates < 88%.
^‡Used an awk command to remove variants with average GQ < 35.
^¥Filtered VQSR processed variants at the 99% sensitivity tranche.

ISSN: 1471-2105