nf-core · Jakob37 · Jan 20, 2026 · Jan 15, 2026 · Jan 19, 2026 · Jan 19, 2026
diff --git a/data/genomics/homo_sapiens/README.md b/data/genomics/homo_sapiens/README.md
@@ -579,6 +579,75 @@ This dataset contains:
 
 This folder contains `AnnotFilterRule.pm` which comes from [The Broad](https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm) and is used for filtering in `starfusion`. 
 
+### Gens test data
+
+These files are used to test the Gens input preprocessing module. 
+
+#### Binned coverage
+
+This file was obtained from the following WGS processing pipeline: [SMD WGS pipeline](https://github.com/SMD-Bioinformatics-Lund/nextflow_wgs).
+
+`data/genomics/homo_sapiens/illumina/gatk/hg002_chr20_90000_to_100000.standardizedCR.tsv`
+
+The relevant pipeline commands. Inputs is an aligned BAM-file, and an interval file specifying 100bp bins. It also requires a GATK format panel of normal.
+
+```
+gatk CollectReadCounts \\
+   -I $bam -L $params.COV_INTERVAL_LIST \\
+   --interval-merging-rule OVERLAPPING_ONLY -O ${bam}.hdf5
+
+gatk --java-options "-Xmx30g" DenoiseReadCounts \\
+   -I ${bam}.hdf5 --count-panel-of-normals ${PON[sex]} \\
+   --standardized-copy-ratios ${id}.standardizedCR.tsv \\
+   --denoised-copy-ratios ${id}.denoisedCR.tsv
+```
+
+This output is then processed to retrieve only chromsome 20 entries in the positions 90,000 - 100,000.
+
+```
+grep -E "^@|^20" hg002.standardizedCR.tsv | awk '$2 >= 90000 && $2 <= 100000' > hg002_chr20_90000_to_100000.standardizedCR.tsv
+```
+
+#### SNV calls (gGVCF)
+
+This file was obtained from the following WGS processing pipeline: [SMD WGS pipeline](https://github.com/SMD-Bioinformatics-Lund/nextflow_wgs).
+
+`data/genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz`
+
+Output from running DNA-scope on the aligned BAM file and then exacting the range 90000 to 100000 from chromosome 20.
+
+DNAscope is a reimplementation and slight improvement on GATK's HaplotypeCaller.
+
+Using masked hg38 as reference. Using base quality calibrated inputs.
+
+```
+sentieon driver \\
+   -r ${params.genome_file} \\
+   -q $bqsr \\
+   -i $bam \\
+   --algo DNAscope --emit_mode GVCF ${id}.dnascope.gvcf.gz
+```
+
+```
+zcat hg002.dnascope.gvcf.gz | grep -E "^#|^20" | awk '/^#/ || ($2 >= 90000 && $2 <= 100000>)' > hg002_chr20_90000_to_100000.dnascope.gvcf
+bgzip hg002_chr20_90000_to_100000.dnascope.gvcf
+tabix hg002_chr20_90000_to_100000.dnascope.gvcf.gz
+```
+
+#### B-allele frequency sampling locations
+
+* data/genomics/homo_sapiens/illumina/tab/gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz
+
+Subset of the file https://github.com/SMD-Bioinformatics-Lund/gens/releases/download/v4.3.0/gnomad_hg38.0.05.txt.gz
+
+It is based on Gnomad (v2), where locations with an ALT allele frequency >= 0.05 is extracted. This file only contains the locations on these calls (i.e. col 1: chrom, col 2: position).
+
+Then the target range is extracted:
+
+```
+zcat gnomad_hg38.0.05.txt.gz | awk '$1 == 20 && ($2 >= 90000 && $2 <= 100000)' | gzip > gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz
+```
+
 ### Missing files
 
 1. Single-end reads

diff --git a/data/genomics/homo_sapiens/illumina/gatk/hg002_chr20_90000_to_100000.standardizedCR.tsv b/data/genomics/homo_sapiens/illumina/gatk/hg002_chr20_90000_to_100000.standardizedCR.tsv
@@ -0,0 +1,297 @@
+@HD	VN:1.6
+@SQ	SN:1	LN:248956422
+@SQ	SN:2	LN:242193529
+@SQ	SN:3	LN:198295559
+@SQ	SN:4	LN:190214555
+@SQ	SN:5	LN:181538259
+@SQ	SN:6	LN:170805979
+@SQ	SN:7	LN:159345973
+@SQ	SN:8	LN:145138636
+@SQ	SN:9	LN:138394717
+@SQ	SN:10	LN:133797422
+@SQ	SN:11	LN:135086622
+@SQ	SN:12	LN:133275309
+@SQ	SN:13	LN:114364328
+@SQ	SN:14	LN:107043718
+@SQ	SN:15	LN:101991189
+@SQ	SN:16	LN:90338345
+@SQ	SN:17	LN:83257441
+@SQ	SN:18	LN:80373285
+@SQ	SN:19	LN:58617616
+@SQ	SN:20	LN:64444167
+@SQ	SN:21	LN:46709983
+@SQ	SN:22	LN:50818468
+@SQ	SN:X	LN:156040895
+@SQ	SN:Y	LN:57227415
+@SQ	SN:M	LN:16569
+@SQ	SN:1_KI270706v1_random	LN:175055
+@SQ	SN:1_KI270707v1_random	LN:32032
+@SQ	SN:1_KI270708v1_random	LN:127682
+@SQ	SN:1_KI270709v1_random	LN:66860
+@SQ	SN:1_KI270710v1_random	LN:40176
+@SQ	SN:1_KI270711v1_random	LN:42210
+@SQ	SN:1_KI270712v1_random	LN:176043
+@SQ	SN:1_KI270713v1_random	LN:40745
+@SQ	SN:1_KI270714v1_random	LN:41717
+@SQ	SN:2_KI270715v1_random	LN:161471
+@SQ	SN:2_KI270716v1_random	LN:153799
+@SQ	SN:3_GL000221v1_random	LN:155397
+@SQ	SN:4_GL000008v2_random	LN:209709
+@SQ	SN:5_GL000208v1_random	LN:92689
+@SQ	SN:9_KI270717v1_random	LN:40062
+@SQ	SN:9_KI270718v1_random	LN:38054
+@SQ	SN:9_KI270719v1_random	LN:176845
+@SQ	SN:9_KI270720v1_random	LN:39050
+@SQ	SN:11_KI270721v1_random	LN:100316
+@SQ	SN:14_GL000009v2_random	LN:201709
+@SQ	SN:14_GL000225v1_random	LN:211173
+@SQ	SN:14_KI270722v1_random	LN:194050
+@SQ	SN:14_GL000194v1_random	LN:191469
+@SQ	SN:14_KI270723v1_random	LN:38115
+@SQ	SN:14_KI270724v1_random	LN:39555
+@SQ	SN:14_KI270725v1_random	LN:172810
+@SQ	SN:14_KI270726v1_random	LN:43739
+@SQ	SN:15_KI270727v1_random	LN:448248
+@SQ	SN:16_KI270728v1_random	LN:1872759
+@SQ	SN:17_GL000205v2_random	LN:185591
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+@SQ	SN:22_KI270739v1_random	LN:73985
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+@SQ	SN:Un_KI270312v1	LN:998
+@SQ	SN:Un_KI270311v1	LN:12399
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+@SQ	SN:Un_KI270423v1	LN:981
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+@SQ	SN:Un_GL000218v1	LN:161147
+@SQ	SN:EBV	LN:171823
+@RG	ID:GATKCopyNumber	SM:hg002
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diff --git a/data/genomics/homo_sapiens/illumina/tab/gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz b/data/genomics/homo_sapiens/illumina/tab/gnomad_hg38_chr20_90000_to_100000.0.05.txt.gz
diff --git a/data/genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz b/data/genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz
diff --git a/data/genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz.tbi b/data/genomics/homo_sapiens/illumina/vcf/hg002_chr20_90000_to_100000.dnascope.gvcf.gz.tbi