Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data

BMC Genomics

Table 2 Effects of data preprocessing on SNP calling accuracy

raw: without any preprocessing steps; filterY: removing those reads that fail the Illumina chastity filter; trim: trimming off low-quality tails from reads with the BWA parameter (-q 15); filterY&trim: removing those reads that fail the Illumina chastity filter and trimming off low quality tails. SNPs were called for five samples together by GATK using bases with base quality≥20 and reads with mapping quality ≥20. Only sites with QUAL > = 50 were considered as potentially variable sites.

ISSN: 1471-2164