Benchmarking variant identification tools for plant diversity discovery

BMC Genomics

Table 1 Summary of SNPs identified by combinations of aligners and variant calling programs

	Unfiltered SNPs				Filtered SNPs
	Total	Domesticated tomatoes	Wild tomatoes	Common	Total	Domesticated tomatoes	Wild tomatoes	Common
BWA-MEM + GATK-HC	131,449,946	17,771,072	128,294,973	14,616,099	93,739,759	13,628,974	91,482,115	11,371,330
Bowtie2-tuned + GATK-HC	73,393,338	11,813,500	70,453,383	8,873,545	30,307,811	8,261,729	28,243,136	6,197,054
BWA-MEM + SAMtools-mpileup	133,734,683	17,268,821	130,886,221	14,420,359	80,709,232	10,366,835	78,727,565	8,385,168
Bowtie2-tuned + SAMtools-mpileup	69,219,499	12,390,916	66,416,422	9,587,839	46,436,709	8,832,598	44,626,459	7,022,348

ISSN: 1471-2164