Skip to main content
Figure 4 | BMC Bioinformatics

Figure 4

From: ANGSD: Analysis of Next Generation Sequencing Data

Figure 4

Overlap between inferred SNPs with a critical p-value threshold of 10 -6and not using BAQ. Venn diagram of the overlap between the SNP discovery for ANGSD, GATK and SAMtools for 33 CEU samples for chromosome 1. We used default parameters with GATK for SAMtools we discarded reads with a mapping quality below 10. For ANGSD we choose an p-value threshold of 10−6 and didn’t enable BAQ. In A, we used the SAMtools genotype likelihood model in ANGSD, in B we used the GATK model in ANGSD.

Back to article page