Drysdale WGS vs IWGSC RefSeq v1.0 Genome Assembly
datasetposted on 10.07.2018 by Nathan Watson-Haigh, Radoslaw Suchecki, Melissa de Oliveira Santos Garcia, Elena Kalashyan, Ute Baumann
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
WGS reads of Drysdale (http://dx.doi.org/10.1111/j.1467-7652.2012.00717.x) were aligned against the IWGSC Triticum aestivum Chinese Spring RefSeq v1.0 genome assembly using Minimap2. These BAM files (.bam) and index files (.bam.bai) are provided together with a summary of read alignment coverage bigWig files (.bam.bw). SNP variants were called from these BAM files to generate VCF files (.bam.vcf.gz) and index files (.bam.vcf.gz.tbi) and are provided together with a summary of SNP density (SNPs per 10 kbp) bigWig files (.bam.vcf.w10000_s10000.bw). VCF files contain the following filter values and corresponding meaning: PASS = high quality (Q>=30) homozygous; Het = high quality (Q>=30) heterozygous; LowQualHom = low quality (Q<30) homozygous; LowQualHet = low quality (Q<30) heterozygous. Files are provided separately for each chromosome part.