Andrew

SURVIVOR filter based on AF has no effect

4

Hi, I have Manta VCFs >100 individuals that I've merged using SURVIVOR merge with this command: ``` SURVIVOR merge sample_files.txt 1000 1 1 1 0 0 Manta_merged.vcf ``` Then I...

Half-siblings are treated as full siblings

7

I noticed that in a pedigree I analyzed where two individuals are half-siblings (same mother), they were classified as sib-sib (0.50), but they cluster with the individuals who are uncle/aunt-niece...

**Preferred term label:** Bacterial encephalitis **Synonyms** **Definition (free text, please give PubMed ID)** Encephalitis caused by bacterial infection (?). A few papers mentioning this term: - PMID: [31525232](https://www.ncbi.nlm.nih.gov/pubmed/31525232) - https://www.thelancet.com/journals/lancet/article/PIIS1473-3099(10)70222-X/fulltext...

Compound heterozygous gene in father and child not prioritized in trio analysis

8

Hi, I have a trio where the father and daughter are both compound heterozygous for the known causal gene (autosomal) but Exomiser is not prioritizing the gene. When I run...

Use LOCAL db for initial frequency filtering but not for inheritance mode filter

6

I recently started testing using a LOCAL to capture and remove platform-specific false positive variants. Basically, we have exomes for about 1000 individuals and sometimes we find "novel" variants (i.e.,...

Hi, I noticed recently that when I use `vt estimate` command, the QUAL score is convert to `-nan` for multi-allelic sites. This is fine with variants with single allele. An...

bcftools annotate using large annotation VCF is slow regardless of input VCF size

11

Hi, I'm trying to annotate a VCF with only 248 variants using the gnomad genomes VCF as annotation and it takes about 2 hours to run. Both the input VCF...

'=' sign in VEP CSQ field results in error

3

Hi, I have recently started adding more annotations from VEP to my VCF and noticed that when I add MutPred2 (dbNSFP 2.9.3) that I get an error in Gemini, likely...

Add CADD InDels

1

It would be nice to include indels with CADD scores in the gemini annotation pipeline. http://krishna.gs.washington.edu/download/CADD/v1.3/InDels.tsv.gz ``` zcat InDels.tsv.gz | head ## CADD v1.3 (c) University of Washington and Hudson-Alpha...

Gemini annotate using VCF with AF_POPMAX=1 results in error

7

I'm using Gemini 0.19.1 with the gnomAD exomes VCF file, trying to extract the AF_POPMAX field and I'm getting an error: ``` gemini annotate '-f' '/data/gnomad/gnomad.exomes.r2.0.1.sites.vt.vcf.gz' '-c' 'aaf_gnomad_ex,af_popmax_ex,popmax_ex' '-a' 'extract'...