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Combined display of all available logs of 22126. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 14:26, 8 January 2025 Gabre talk contribs created page SNP calling exercise answers part 2 (Created page with " '''Q1''' First running: <pre> gatk VariantFiltration -V NA24694.vcf.gz -O NA24694_hf.vcf.gz -filter "DP < 10.0" --filter-name "DP" -filter "QUAL < 30.0" --filter-name "QUAL30" -filter "SOR > 3.0" --filter-name "SOR3" -filter "FS > 60.0" --filter-name "FS60" -filter "MQ < 40.0" --filter-name "MQ40" </pre> and <pre> bcftools view -H NA24694_hf.vcf.gz |grep -v PASS |wc -l </pre> Gives us 4005 sites. <pre> bcftools view -H --type=...")
- 17:28, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 2 answers (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...")
- 17:27, 15 December 2024 Gabre talk contribs created page SNP calling exercise part 1 answers (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...")
- 18:20, 10 December 2024 Gabre talk contribs created page Unix pipes (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...")
- 16:06, 29 November 2024 Gabre talk contribs created page SNP calling exercise part 2 (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...")
- 15:35, 29 November 2024 Gabre talk contribs created page SNP calling exercise answers part 1 (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...")