Sequence variations data on 292 pigeonpea lines for understanding genetic relationships and genome-wide association

This data contains sequence variation information on 292 pigeonpea lines. The sequence variations were obtained through paired-end sequencing on an Illumina HiSeq 2000 sequencer. Paired-end resequencing reads were mapped using BWA7 (ver. 0.5.9) with default parameters onto the pigeonpea reference genome. Mapped reads were converted into BAM files using SAMtools (ver. 0.1.18), and duplicate reads were removed with SAMtools. Genome coverage of mapped reads on the reference genome was estimated using GATK (ver. 1.4-11). After removing duplicate reads, variants including SNPs and indels were detected using BCFtools (ver. 0.1.17) in SAMtools. Captured variants were annotated with ANNOVAR (ver. 2011Nov28) and SnpEff (ver. 3.2). For these variants, SNPs were counted with VCFtools (ver. 0.1.10) and a hapmap file has been provided here. Sequencing data generated have been submitted to https://www.ncbi.nlm.nih.gov/bioproject/?term=383013.