Resources bundle for somatic workflow using HiFi reads

The following files are included in the "hifisomatic_resources.tar.gz" resource bundle.

├── chr.bed
├── GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta
├── GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta.fai
├── human_GRCh38_no_alt_analysis_set.trf.bed
├── refFlat.hg38.txt
├── sniffles_all_non_germline.nosamples.vcf.gz
└── sniffles_all_non_germline.nosamples.vcf.gz.tbi

For the Sniffles non_germline VCF, please cite the Human Pangenome Project paper: https://www.nature.com/articles/s41586-022-04601-8. Briefly, Sniffles 2.0.7 were used to generate a joint-call VCF from 118 control samples with the "--non-germline" flag (all other parameters remain default). "human_GRCh38_no_alt_analysis_set.trf.bed" was downloaded from https://github.com/PacificBiosciences/pbsv/blob/master/annotations/human_GRCh38_no_alt_analysis_set.trf.bed. "GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta" was obtained from Wagner, J. et al. (Nat Biotechnol 2022). "chr.bed" is simply the start and end coord of each chromosome and was created manually using the genome size from the fasta index.

In addition, the repo contains two small demo dataset to test the workflow:

"COLO829.30X.SV_region.bam" and "COLO829BL.30X.SV_region.bam" contains region in COLO829 cell lines that has 57 (out of 62) truth SV from Valle-Inclan et. al. 2022. "HCC1395.chr20.30X.bam" and "HCC1395BL.chr20.30X.bam" contains the chr20 region of HCC1395 cell lines.