Computational protocol: Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing

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Protocol publication

[…] Paired-end reads were aligned to the TAIR10 () reference genome with the use of Bowtie2 (). Mapped reads were reformatted with the mpileup function of SAMtools (), and the allele frequencies at polymorphic sites with Phred quality score of >20 and coverage >500 were counted by varScan2 ().The G-test was used to detect the SNP markers whose Sha/Tsu-1 ratio between two bulk populations significantly differed. To reduce the random binomial sampling noise of two alleles introduced by sequencing, the smoothed G test (G′ test) () was performed at each SNP marker position with a sliding window of 9 Mb (∼36 cM as determined in Results section) and the tri-cube weight function (). […]

Pipeline specifications

Software tools Bowtie2, SAMtools, VarScan
Databases TAIR
Application WGS analysis
Organisms Arabidopsis thaliana, Homo sapiens