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- 16:28, 15 December 2024 SNP calling exercise part 2 answers (hist | edit) [1,960 bytes] Gabre (talk | contribs) (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
- 16:27, 15 December 2024 SNP calling exercise part 1 answers (hist | edit) [3,647 bytes] Gabre (talk | contribs) (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
- 17:20, 10 December 2024 Unix pipes (hist | edit) [27,039 bytes] Gabre (talk | contribs) (Created page with "Welcome! This small guide contains a lot of information and examples that will help you as you start learning Linux. In addition to simple Linux commands, this tutorial also provides three Python scripts, that you can run and try out the concepts yourself. # Basic Unix Commands and Concepts This is where your journey begins! If you are new to Unix-based systems and also got used to Windows or MacOS, you really need a brief explanation of a few key commands and concept...")
- 15:06, 29 November 2024 SNP calling exercise part 2 (hist | edit) [6,329 bytes] Gabre (talk | contribs) (Created page with " <H2> Filtering</H2> We saw that the data contains some calls of poor quality. Ideally, we do not want to carry over these calls into downstream analyses. We will explore how to filter out genotype data. <H3> Hard filtering </H3> A major downside of soft filtering is that does not apply for samples for which we do not have a good representation of the genetic diversity. An alternative is to do hard filtering meaning filtering the variants according to predetermined...")
- 14:35, 29 November 2024 SNP calling exercise answers part 1 (hist | edit) [3,647 bytes] Gabre (talk | contribs) (Created page with "'''Q1''' First, running: <pre> tabix -f -p vcf NA24694.gvcf.gz </pre> then <pre> gatk --java-options "-Xmx10g" HaplotypeCaller -R /home/databases/references/human/GRCh38_full_analysis_set_plus_decoy_hla.fa -I /home/projects/22126_NGS/exercises/snp_calling/NA24694.bam -L chr20 -O NA24694.gvcf.gz --dbsnp /home/databases/databases/GRCh38/Homo_sapiens_assembly38.dbsnp138.vcf.gz -ERC GVCF </pre> <pre> gatk GenotypeGVCFs -R /home/databases/references/human/GRCh3...")
- 14:33, 29 November 2024 SNP calling exercise part 1 (hist | edit) [6,381 bytes] Gabre (talk | contribs) (Created page with "<H2>Overview</H2> First: <OL> <LI>Navigate to your home directory: <LI>Create a directory called "variant_call" <LI>Navigate to the directory you just created. </OL> We will: <OL> <LI>Genotype some whole-genome sequencing data. <LI>Get acquainted with VCF files <LI>Soft filtering <LI>Hard filtering <LI> Annotation of variants </OL> ---- <H2>Genotyping</H2> We will genotype a chromosome from a BAM file that has been processed using the steps we detailed before. It i...")
- 15:40, 14 November 2024 Unix notes (hist | edit) [3,924 bytes] Gabre (talk | contribs) (Created page with "Certainly! Here's a Markdown version of the UNIX instructions from the provided PDF: # Using UNIX UNIX primarily operates through a command-line interface, allowing users to execute commands directly. While this may initially seem less intuitive than graphical interfaces, its power becomes evident with experience. ## Obtaining UNIX There are various methods to access UNIX: - **Windows**: Download and install [MobaXTerm](https://mobaxterm.mobatek.net/). - **Mac**: ma...")
- 14:29, 7 November 2024 Program 2025 (hist | edit) [13,535 bytes] Gabre (talk | contribs) (Created page with " '''REMEMBER TO BRING A LAPTOP FOR EXERCISES''' Lectures will be in person in building [https://goo.gl/maps/k4wYkMjTJ2HLHuyN8 303A] in auditorium 44. Offline discussions will take place on Discord (https://discord.gg/7PKuKhKYQJ). Please register with your '''full name'''. Will use Discord for online classes and collaboration with your project partners. <!-- Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your ful...")