Comparison of sequencing data processing pipelines and application to underrepresented African human populations

BMC Bioinformatics

Table 2 Overview of the steps in 29 HTS studies

Study	Indel realignment	BQSR^BP	HC^BP	UG	Other variant caller	VQSR^BP	Hard filtering
[12]	No	No	No	No	Yes	No	Yes
[13]	Yes	No	No	No	Yes	No	Yes
[8]	Yes	Yes	NA	NA	NA	NA	NA
[14]^#	Yes	Yes	Yes	No	No	Yes	No
[15]	Yes	Yes	Maybe¹	Maybe¹	No	No	Yes
[16]	No	No	Yes	No	Yes	No	Yes
[17]	Yes	Yes	No	Yes	Yes	Yes	No
[18]	Yes?²	Yes?²	Maybe¹	Maybe¹	No	No	Yes
[19]	NA	NA	No	No	Yes	NA	NA
[20]	Yes	No	No	No	Yes	No	Yes
[21]	No	No	No	Yes	No	No	No
[22]	No	No	No	No	Yes	No	No
[23]^#	No	Yes	Yes	No	No	Yes	No
[24]^#	Yes (other)²	Yes	Yes	No	Yes	Yes	Yes
[25]	Yes	Yes	Yes	No	No	No	No
[26]	Yes (NA)²	Yes (NA)²	No	Yes	No	No	Yes
[27]	Yes	Yes	No	No	Yes	No	Yes
[28] cohort 1	No	Yes (other)²	No	No	Yes	No	Yes
[28] cohort 2	No	No	Yes	No	No	Yes	Yes
[29]^#	Yes	Yes	Yes	No	No	Yes	Yes
[30]	No	No	No	Yes	No	No	No
[31]	Yes	Yes	No	Yes	No	Yes	No
[32]	Yes	Yes	No	Yes	No	Yes	No
[33]	No	No	Yes	No	No	Yes	Yes
[34]*	Yes	Yes	No	Yes	No	No	Yes
[35]*	Yes	Yes	No	Yes	No	No	Yes
[36]*^#	No	Yes	Yes	No	No	Yes	No
[37]*^#	No	Yes	Yes	No	No	Yes	No
[38]*	Yes	No	Yes	No	No	No	Yes
[39]*	Yes	Yes	Yes	No	No	No	Yes

BQSR Base Quality Score Recalibration, HC HaplotypeCaller + GenotypeGVCFs, VQSR Variant Quality score Recalibration, UG UnifiedGenotyper
^BPGATK tool in the Best Practices in 2019
^*Species other than human
^#Reports using BQSR, HC + GenotypeGVCFs and VQSR
¹Uncertainty as to which GATK variant caller was used (HC or UG)
²Various uncertainties or use of alternative software for indel realignment or BQSR

ISSN: 1471-2105