Glucoma-variant-calling

Please find the following files:

• Project abstract is in the file named "GlaucomaVC _abstract.pdf".
• raw data links are in the file named "links".
• Commands and steps for each team member is assigned as the member name (Samah, Dalia,Fayrouz, Marwa Abd elazim, Marwa Aswa) and the samples names are SRR5858162, SRR5858161, SRR5858157, SRR5858204 and SRR5858160 respectively.
• The project Report is in file names "Report file".
• The FastQC file for each sample reads is assigned as (samplename_1.html, samplename_2.html).
• The Mapping QC stat is in the file named "samplename.stat".
  • The BaseRecalibrator report is in the file named "samplename.report".
• Markduplicates is in the sample named "samplename.txt".
• The gvcf files for each sample coud not be uploaded on Github, so we uploaded them to the same Google drive folder on the following link: https://drive.google.com/open?id=1imcVlxzXwxJUBJr2HziMLekziK3kbPrH
• Joint variant calling VCF statistics file is named "stats.txt".
• The figures of the different filtrations for SNPs and indels is in file named (GATK figures.rar).
• please ckek the issues.
• note: Special thanks for Dr.Tamer great efforts and for eng. Mohamed efforts in the machine troubleshoting.