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17 December 2024
16 December 2024
15 December 2024
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N 16:28 | SNP calling exercise part 2 answers 2 changes history +1,960 [Gabre (2×)] | |||
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16:28 (cur | prev) −5,305 Gabre talk contribs | ||||
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16:28 (cur | prev) +7,265 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...") | |||
| N 16:27 | SNP calling exercise part 1 answers diffhist +3,647 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 | SNP calling exercise part 1 diffhist +50 Gabre talk contribs | ||||
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16:27 | SNP calling exercise part 2 2 changes history +118 [Gabre (2×)] | |||
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16:27 (cur | prev) +2 Gabre talk contribs | ||||
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16:25 (cur | prev) +116 Gabre talk contribs | ||||
10 December 2024
| N 17:20 | Unix pipes diffhist +35,163 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...") | ||||
29 November 2024
| N 15:06 | SNP calling exercise part 2 diffhist +6,211 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...") | ||||
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N 14:52 | SNP calling exercise answers part 1 2 changes history +3,647 [Gabre (2×)] | |||
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14:52 (cur | prev) −975 Gabre talk contribs | ||||
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14:35 (cur | prev) +4,622 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...") | |||
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N 14:36 | SNP calling exercise part 1 2 changes history +6,331 [Gabre (2×)] | |||
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14:36 (cur | prev) +67 Gabre talk contribs | ||||
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14:33 (cur | prev) +6,264 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...") | |||
| 14:27 | Program 2025 diffhist +46 Gabre talk contribs | ||||
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14:02 | Denovo solution 2 changes history +523 [Gabre (2×)] | |||
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14:02 (cur | prev) +203 Gabre talk contribs | ||||
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13:55 (cur | prev) +320 Gabre talk contribs | ||||
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13:55 | Denovo exercise 5 changes history +1,091 [Gabre (5×)] | |||
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13:55 (cur | prev) +1 Gabre talk contribs | ||||
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13:55 (cur | prev) +1 Gabre talk contribs | ||||
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13:54 (cur | prev) +1,071 Gabre talk contribs | ||||
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13:03 (cur | prev) +2 Gabre talk contribs | ||||
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11:16 (cur | prev) +16 Gabre talk contribs | ||||
28 November 2024
| 15:49 | Denovo solution diffhist −18 Gabre talk contribs | ||||
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15:49 | Denovo exercise 6 changes history +293 [Gabre (6×)] | |||
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15:49 (cur | prev) +2 Gabre talk contribs | ||||
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15:46 (cur | prev) +129 Gabre talk contribs | ||||
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15:43 (cur | prev) +30 Gabre talk contribs | ||||
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15:39 (cur | prev) +37 Gabre talk contribs | ||||
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15:37 (cur | prev) +28 Gabre talk contribs | ||||
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15:36 (cur | prev) +67 Gabre talk contribs | ||||