nf-cmgg-test-datasets

Test datasets for unit tests with the nf-cmgg pipelines

data/genomics/homo_sapiens/illumina/cram/SVcontrol

SVcontrol: subsetted crams for testing of nf-cmgg-structural

• testSV.PosCon1.cram sample with a homozygous deletion upstream of CHST6 (hg38.chr16:75,500,000-75,538,999). Reads subsetted chr16:75,000,000-75,600,000. Sib of PosCon2.cram.
• testSV.PosCon2.cram sample with a homozygous deletion upstream of CHST6 (hg38.chr16:75,500,000-75,538,999). Reads subsetted chr16:75,000,000-75,600,000. Sib of PosCon1.cram.
• testSV.PosCon3.cram sample with a homozygous deletion in TTLL5 (hg38.chr14:75,771,149-75,772,647). Reads subsetted chr14:75,400,000-76,000,000.
• testSV.PosCon4.cram sample with two heterozygous deletion on chrX with uncertain boundaries (hg38.chrX:154,097,604-154,154,739 and chrX:153,773,230-153,776,214). Reads subsetted chrX:153,400,000-154,000,000.

data/genomics/homo_sapiens/illumina/bed/SVcontrol

SVcontrol: region of interest bed for testing of nf-cmgg-structural

• testSV.PosCon1and2.roi.bed bed file for chr16:74,949,851-75,608,957 with Ensembl Transcript IDs.
• testSV.PosCon3.roi.bed bed file for chr14:75,294,403-76,014,143 with Ensembl Transcript IDs.
• testSV.PosCon4.roi.bed bed file for chrX:153,396,962-154,014,377 with Ensembl Transcript IDs.