Using CHM13 as a reference

[steven-solar]

Is it possible to use CHM13 as a reference for AnnotSV? Even if current annotations are just lifted from GRCh38 to CHM13 it would be very useful. Thank you!

[lgmgeo]

Hi @steven-solar,

Absolutely, it's planned.
The next version with updated annotations shall integrate the T2T-CHM13 build.
Sorry for the delay,

Best,
Véronique

[georgiesamaha]

hi @lgmgeo, just wondering if you have a sense of roughly when the CHM13 build might be implemented? Would love to use it on a current project.

Cheers,
Georgie

[lgmgeo]

Hi Georgie,

Really sorry because new ideas/features to investigate in AnnotSV are piling up... and currently I can't achieve everything
(not to mention that I don't work full time on AnnotSV).

I'm not able to give you a precise date for this update.
I apologize for the inconvenience.

Thank you for your interest in AnnotSV,
Best,
Véronique

[georgiesamaha]

No problem at all @lgmgeo, I understand. Thanks for letting me know :)

Looking forward to using AnnotSV with CHM13 when its ready, its a great tool!

[lgmgeo]

Thank you for your understanding and kindness!

[quanc1989]

Just wondering how is going on with CHM13-T2T?

[lgmgeo]

Sorry, I haven't started yet. But I always have it in mind.

[quanc1989]

@lgmgeo Thank you for this useful tool. I think it would be more widely used if it provided a way to create new references by user.

[lgmgeo]

Any user interested in implementing new annotations/features in AnnotSV is welcome ;o)
Please do not hesitate to fork the code and open a pull request.

[lgmgeo]

The most time-consuming thing for me would be:

• To search for download the different T2T-CHM13 files available (I'm not used to working with this genome build)
• Then to lifted from GRCh38 to T2T-CHM13 the others one

As most of the annotation files are not available in T2T-CHM13, this is really an obstacle to providing you this build in AnnotSV.

Here is the (incomplete) list of the GRCh38 files needed to be available in T2T-CHM13:

The most important (files must be downloaded in T2T-CHM13):

• RefSeq gene annotations:
  http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz
• ENSEMBL gene annotations:
  http://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.chr.gtf.gz
• GC content annotations
  http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromFa.tar.gz
• Repeated sequences annotations
  Ok, available at UCSC
• Segmental duplication annotations
  Ok, available at UCSC
• GAP annotations
  Ok, available at UCSC
• Cytoband
  http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz

Others (liftover from GRCh38 to T2T-CHM13):

• ClinVar pathogenic SV annotations
  https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20240215.vcf.gz
• Dosage sensitive genes/regions annotation (ClinGen)
  ftp://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
  ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv
• dbVarNR pathogenic SV annotations
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh38.nr_deletions.pathogenic.tsv.gz
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/GRCh38.nr_duplications.pathogenic.tsv.gz
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh38.nr_insertions.pathogenic.tsv.gz
• Known pathogenic SNV/indel annotations
  https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20240215.vcf.gz
• gnomAD benign SV annotations
  https://gnomad.broadinstitute.org/downloads#v4-structural-variants
• ClinVar benign SV annotations
  https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20240215.vcf.gz
• Not dosage sensitive genes/regions annotation (ClinGen)
  https://ftp.clinicalgenome.org/ClinGen_gene_curation_list_GRCh38.tsv
  https://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv
• DGV benign SV annotations
  http://dgv.tcag.ca/dgv/docs/GRCh38_hg38_variants_2020-02-25.txt
• DDD benign SV annotations
  https://www.deciphergenomics.org/files/downloads/population_cnv_grch38.txt.gz
• 1000 genomes benign SV annotations
  http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/supporting/GRCh38_positions/ALL.wgs.mergedSV.v8.20130502.svs.genotypes.GRCh38.vcf.gz
• dbVar benign SV annotations
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/deletions/GRCh38.nr_deletions.common.bed.gz
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/duplications/GRCh38.nr_duplications.common.bed.gz
  https://ftp.ncbi.nlm.nih.gov/pub/dbVar/sandbox/sv_datasets/nonredundant/insertions/GRCh38.nr_insertions.common.bed.gz
  ...

If anyone can help me to find the ones available in CHM13-T2T (at least the most important), that would be great.