Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra

BMC Genomics

Table 1 Number of variants detected for each of the 7 calling modalities tested in the present study

Variant calling modality	Missing value in genotype calls
	noNA	2NA	anyNA
GATK	464,829	555,828	902,256
gVCF_GATK	407,037	497,314	927,522
FreeBayes	492,073	640,445	795,459
Mpileup	496,688	594,932	949,411
3Callers	341,584	366,123	400,392
4Callers	252,887	262,447	271,399
3CallersConsensus	356,275	442,931	785,377

“noNA”: no missing value; “2NA”: lower or equal to 2 missing values; “anyNA”: no filter on missing values. “3Callers”: SNPs detected with at least 3 callers; “4Callers”: SNPs detected with 4 callers; “3CallersConsensus”: SNPs detected with at least 3 callers with correction of the genotype calling when discrepancies existed between callers (see details in Methods)

ISSN: 1471-2164