MediaWiki API result
This is the HTML representation of the JSON format. HTML is good for debugging, but is unsuitable for application use.
Specify the format parameter to change the output format. To see the non-HTML representation of the JSON format, set format=json.
See the complete documentation, or the API help for more information.
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{
"logid": 113,
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"title": "Exercise",
"pageid": 87,
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"params": {},
"type": "create",
"action": "create",
"user": "Rasmus",
"timestamp": "2025-12-12T13:19:11Z",
"comment": "Created page with \"fefefeefefefefefe\""
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"title": "User:Rasmus",
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"user": "WikiSysop",
"timestamp": "2025-12-12T13:09:16Z",
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{
"logid": 111,
"ns": 0,
"title": "Advanced UNIX and Pipes",
"pageid": 86,
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"user": "Mick",
"timestamp": "2025-11-20T09:03:46Z",
"comment": "Created page with \"== Advanced UNIX and Pipes == This page covers standard input/output streams, redirection, pipes, file descriptors, and examples using Python scripts. These concepts are extremely useful in NGS analysis (e.g., chaining commands together, avoiding intermediate files, streaming FASTQ/BAM data, etc.). === stdout, stdin, stderr === Every UNIX command uses three data streams: * '''stdin''' (file descriptor 0) \u2013 input * '''stdout''' (file descriptor 1) \u2013 normal output...\""
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{
"logid": 110,
"ns": 0,
"title": "Basic UNIX notes",
"pageid": 85,
"logpage": 85,
"revid": 216,
"params": {},
"type": "create",
"action": "create",
"user": "Mick",
"timestamp": "2025-11-20T09:02:38Z",
"comment": "Created page with \"=== Introduction to UNIX === UNIX refers to a family of multitasking, multi-user operating systems that originated from AT&T Unix (Bell Labs, 1969). Many modern operating systems are UNIX-like and inherit its core principles of stability, flexibility, and powerful command-line tools. Although UNIX may appear complex at first, it is essential in bioinformatics and NGS analysis. Most tools you will use in this course (and in real research) run exclusively on the command l...\""
},
{
"logid": 109,
"ns": 0,
"title": "Unix Exercises",
"pageid": 84,
"logpage": 84,
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"type": "create",
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"user": "Mick",
"timestamp": "2025-11-19T14:43:29Z",
"comment": "Created page with \"__NOTOC__ {| width=500 style=\"font-size: 10px; float:right; margin-left: 10px; margin-top: -56px;\" |Previous: None |Next: [[Python Recap and Objects]] |} You did complete the [[Course preparation]], right? Otherwise, all of this will fail. == Required course material for the lesson == PowerPoint: [https://teaching.healthtech.dtu.dk/material/22113/22113_01-Unix.ppt Introduction to Unix] The videos are not entirely in sync with the updated PowerPoint. Video: [https:...\""
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{
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"title": "Program 2026",
"pageid": 83,
"logpage": 83,
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"params": {},
"type": "create",
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"user": "Mick",
"timestamp": "2025-11-19T08:23:35Z",
"comment": "Created page with \" '''NOTE: THIS PAGE IS UNDER CONSTRUCTION WITH A NEW TEACHER IN 2026''' '''REMEMBER TO BRING A LAPTOP FOR EXERCISES''' Lectures will be in person in building [https://maps.app.goo.gl/wH5EW199wrChCmWK7 341] in auditorium 23. <!-- Lectures and exercises will take place on Discord (https://discord.gg/FBb2edFW). Please register with your full name. Will use Discord for online classes and collaboration with your project partners. --> The course has two main parts, the...\""
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"user": "WikiSysop",
"timestamp": "2025-08-25T10:05:23Z",
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{
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"ns": 0,
"title": "SNP calling exercise answers part 2",
"pageid": 82,
"logpage": 82,
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"params": {},
"type": "create",
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"user": "Gabre",
"timestamp": "2025-01-08T12:26:42Z",
"comment": "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=...\""
},
{
"logid": 105,
"ns": 0,
"title": "SNP calling exercise part 2 answers",
"pageid": 81,
"logpage": 81,
"revid": 151,
"params": {},
"type": "create",
"action": "create",
"user": "Gabre",
"timestamp": "2024-12-15T15:28:16Z",
"comment": "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...\""
},
{
"logid": 104,
"ns": 0,
"title": "SNP calling exercise part 1 answers",
"pageid": 80,
"logpage": 80,
"revid": 150,
"params": {},
"type": "create",
"action": "create",
"user": "Gabre",
"timestamp": "2024-12-15T15:27:53Z",
"comment": "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...\""
}
]
}
}