User contributions for Gabre

29 November 2024

• 15:0615:06, 29 November 2024 diff hist +6,211‎ N 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..." current
• 14:5214:52, 29 November 2024 diff hist −975‎ SNP calling exercise answers part 1 ‎No edit summary current
• 14:3614:36, 29 November 2024 diff hist +67‎ SNP calling exercise part 1 ‎No edit summary current
• 14:3514:35, 29 November 2024 diff hist +4,622‎ N 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..."
• 14:3314:33, 29 November 2024 diff hist +6,264‎ N SNP calling exercise part 1 ‎ 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..."
• 14:2714:27, 29 November 2024 diff hist +46‎ Program 2025 ‎No edit summary current
• 14:0214:02, 29 November 2024 diff hist +203‎ Denovo solution ‎No edit summary current
• 13:5513:55, 29 November 2024 diff hist +320‎ Denovo solution ‎No edit summary
• 13:5513:55, 29 November 2024 diff hist +1‎ Denovo exercise ‎No edit summary current
• 13:5513:55, 29 November 2024 diff hist +1‎ Denovo exercise ‎No edit summary
• 13:5413:54, 29 November 2024 diff hist +1,071‎ Denovo exercise ‎No edit summary
• 13:0313:03, 29 November 2024 diff hist +2‎ Denovo exercise ‎No edit summary
• 11:1611:16, 29 November 2024 diff hist +16‎ Denovo exercise ‎No edit summary

28 November 2024

• 15:4915:49, 28 November 2024 diff hist −18‎ Denovo solution ‎No edit summary
• 15:4915:49, 28 November 2024 diff hist +2‎ Denovo exercise ‎No edit summary
• 15:4615:46, 28 November 2024 diff hist +129‎ Denovo exercise ‎No edit summary
• 15:4315:43, 28 November 2024 diff hist +30‎ Denovo exercise ‎No edit summary
• 15:3915:39, 28 November 2024 diff hist +37‎ Denovo exercise ‎No edit summary
• 15:3715:37, 28 November 2024 diff hist +28‎ Denovo exercise ‎No edit summary
• 15:3615:36, 28 November 2024 diff hist +67‎ Denovo exercise ‎No edit summary
• 15:3515:35, 28 November 2024 diff hist +37‎ Denovo exercise ‎No edit summary
• 15:3215:32, 28 November 2024 diff hist +31‎ Denovo exercise ‎No edit summary
• 15:1615:16, 28 November 2024 diff hist +28‎ Denovo solution ‎No edit summary
• 15:1615:16, 28 November 2024 diff hist +4‎ Denovo exercise ‎No edit summary
• 15:0015:00, 28 November 2024 diff hist +29‎ Denovo exercise ‎No edit summary
• 14:5814:58, 28 November 2024 diff hist +6‎ Denovo exercise ‎No edit summary
• 13:2313:23, 28 November 2024 diff hist −69‎ Denovo exercise ‎No edit summary
• 13:2313:23, 28 November 2024 diff hist −299‎ Denovo solution ‎No edit summary
• 13:1913:19, 28 November 2024 diff hist +37‎ Denovo exercise ‎No edit summary
• 13:1313:13, 28 November 2024 diff hist −93‎ Denovo exercise ‎No edit summary
• 13:1113:11, 28 November 2024 diff hist +135‎ Denovo exercise ‎No edit summary
• 13:0913:09, 28 November 2024 diff hist −14‎ Denovo exercise ‎No edit summary
• 13:0713:07, 28 November 2024 diff hist +19‎ Denovo exercise ‎No edit summary
• 13:0713:07, 28 November 2024 diff hist +12‎ Denovo exercise ‎No edit summary
• 13:0413:04, 28 November 2024 diff hist −15‎ Denovo solution ‎No edit summary
• 12:5212:52, 28 November 2024 diff hist +3‎ Denovo exercise ‎No edit summary
• 12:4912:49, 28 November 2024 diff hist −819‎ Denovo exercise ‎No edit summary
• 11:5311:53, 28 November 2024 diff hist +5‎ Denovo exercise ‎No edit summary
• 11:4811:48, 28 November 2024 diff hist −3‎ Denovo exercise ‎No edit summary

27 November 2024

• 15:0115:01, 27 November 2024 diff hist +93‎ Program 2025 ‎No edit summary

15 November 2024

• 15:2315:23, 15 November 2024 diff hist 0‎ Program 2025 ‎No edit summary
• 14:5814:58, 15 November 2024 diff hist −28‎ Program 2025 ‎No edit summary
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• 14:2914:29, 15 November 2024 diff hist +2‎ Program 2025 ‎No edit summary
• 14:2814:28, 15 November 2024 diff hist −2‎ Program 2025 ‎No edit summary

14 November 2024

• 16:0116:01, 14 November 2024 diff hist −28‎ Program 2025 ‎No edit summary
• 15:5915:59, 14 November 2024 diff hist −1‎ Unix notes ‎No edit summary current
• 15:5715:57, 14 November 2024 diff hist +3‎ Unix notes ‎ →‎File Permissions
• 15:5615:56, 14 November 2024 diff hist 0‎ Unix notes ‎ →‎File System Basics
• 15:5615:56, 14 November 2024 diff hist +29‎ Unix notes ‎No edit summary