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

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Title Sequence variations data on 292 pigeonpea lines for understanding genetic relationships and genome-wide association
 
Identifier https://doi.org/10.21421/D2/JQLYUJ
 
Creator Saxena, Rachit
Varshney, Rajeev
Upadhyaya, Hari
Khan, Aamir
Yu, Yue
Kim, Changhoon
Rathore, Abhishek
Kim, Dongseon
Kim, Jihun
An, Shaun
Kumar, Vinay
Ghanta, Anuradha
Yamini, KN
Zhang, Wei
Muniswamy, Sonappa
Kim, Jong-So
Penmetsa, R Varma
Wettberg, Eric
Datta, Swapan
 
Publisher ICRISAT Dataverse
 
Description 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.
 
Subject Agricultural Sciences
Genomics
 
Language English
 
Contributor Rachit K, Saxena
 
Relation Phenotyping data on pigeonpea lines for genome-wide association
https://doi.org/10.21421/D2/UNNTPE
 
Type Genotype