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:

1. Solanum habrochaites PI127826
2. Solanum habrochaites LA1777 (wild-type)
3. Solanum habrochaites LA1777 X-ray mutated to allow self-compatibility

Variant Call Format files (VCF files)

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`).

• SNP mean Depth: 33.78 reads (23,268,139 sites)
• SNP Quality:
  • 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:

vcftools --vcf vcf/PI127826.noInDels.vcf --minDP 34 --minQ 770 --recode --recode-INFO-all --out PI127826.noInDels.filtered