SliderII Results of SNPs concordance comparison to Maq.We used 68 lanes human whole genome shotgun sequencing, WGSS, PET data (real data), a total of 906 million reads sizes from 36 to 42 bases, using each of SliderII and MAQ, we aligned these reads to the human genome hg18 resulting a coverage of about 7.5 X. For each aligner, SNPs are sorted in descending order, using SNPs score for SliderII, and the Phred-like consensus quality score for MAQ. Concordance with Ensembl Variation 50 SNPs is used to compare SNPs calling accuracy.
Biscap and cfdr is a script for determining homozygous and heterozygous positions from an alignment using binomial probabilities from a predicted error rate (BiSCaP) and a method to benchmark the accuracy of this and other alignment/SNP-calling methods (cFDR)
ACCUSA is designed for accurate SNP calling on draft genome sequences.The main objective is to rule out pseudo SNPs where the reference genome has low sequencing base quality. This is obtained using a Bayesian framework considering the base quality values of the resequencing reads as well as the base quality of the reference genome.
ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores
Virmid is a Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha)
UMAKE is a software pipeline to detect SNPs and call their genotypes from a list of BAM files. UMAKE pipeline has been successfully applied in detecting SNPs from many large-scale next-generation sequencing studies.