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Kukri WGS vs IWGSC RefSeq v1.0 Genome Assembly

posted on 2018-07-10, 12:53 authored by Nathan Watson-Haigh, Radoslaw Suchecki, Melissa de Oliveira Santos Garcia, Elena Kalashyan, Ute Baumann
WGS reads of Kukri (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.