DNA-seq of Solanum habrochaites PI127826 and LA1777 DNA (part I)

Illumina paired-end HiSeqX reads from the genomic DNA isolated from young leaves of three plants from S. habrochaites: Solanum habrochaites PI127826 Solanum habrochaites LA1777 (wild-type) Solanum habrochaites LA1777 X-ray mutated to allow self-compatibility <strong>Variant Call Format files (VCF files)</strong> Variants have been called from this DNA-seq file using the Solanum lycopersicum ITAG4.0 genome assembly and a custom-made variant-calling pipeline. This has generated the following S. habrochaites PI127826 VCF file: PI127826.vcf.tar.gz Useful statistics computed with `vcftools` on the VCF file with InDels filtered out (`vcftools --remove-indels`). <strong>SNP mean Depth</strong>: 33.78 reads (23,268,139 sites) <strong>SNP Quality: </strong> Median: 137.9 Mean: 304.2 75th percentile: 568 90th percentile: 770 To be able to call SNPs from RNA-seq data, the GATK RNA-seq SNP discovery workflow can be performed.This workflow requires a high-quality VCF file to serve as the `--known-sites` VCF file when performing GATK Base Quality Score Recalibration. Hence a new file called PI127826.noInDels.filtered.vcf.tar.gz has been generated using VCFtools: <pre><code class="language-bash">vcftools --vcf vcf/PI127826.noInDels.vcf --minDP 34 --minQ 770 --recode --recode-INFO-all --out PI127826.noInDels.filtered</code></pre>