Comments (6)
AnnotSV 3.4 is posted.
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Code was added in the dev branch to integrate the benign SV annotation of "gnomad v4" (GRCh38).
This will soon be distributed with the next annotation release.
I will notify you here as soon as the updated annotations are published
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Hi @gevro,
Yes for sure. It will be updated in the new annotation version (December or January).
Best,
Véronique
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Sorry, I didn't find time to finalize the annotation updates at the end of this busy year.
I have blocked the last 2 weeks of the end of January, it will be done before this deadline.
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FYI:
In gnomAD r4, “Controls and biobanks” correspond only to samples collected specifically as controls for disease studies or samples belonging to biobanks (e.g. BioMe, Genizon) or general population studies (e.g., 1000 Genomes, HGDP, PAGE).
=> Therefore, in AnnotSV, “AF”, “AN” and “N_HOMALT” values are extracted from this collection.
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I'm about to ask the same question and it's great to hear the good news. Thanks!
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Related Issues (20)
- Unusual large memory needed for very large sized coupled BNDs HOT 4
- Why is there never a class 2 in ACMG_class? HOT 1
- CytoBand appear... HOT 3
- MAF in gnomAD HOT 1
- Is there a way to include ensembl_ids and/or hgnc_ids along with gene_name? HOT 3
- New long-read population reference HOT 1
- Question about reverse strand genes HOT 7
- Rogue double quote in PRDM10 HOT 6
- custom bed annotation. overlap within n bases HOT 2
- Multiple column and tab errors with CNVkit vcf output HOT 4
- left gene HOT 15
- Mapping of structural variant to intron or coding regions HOT 2
- exomiser error: connect failed connection refused HOT 2
- vcf errors HOT 1
- AnnotSV passing wrong arguments to variant convert HOT 5
- Keep AnnotSV_ID consistent with SV_chrom HOT 10
- frameshift between full and split mode HOT 5
- UCSC link failed to open the correct position HOT 5
- AnnotSV" line 283 HOT 3
- VCF for false positive deletion and for compund etherozygosity
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