Marc Sturm

Hi, I would like to perform SV calling on human mitochondria. Since this chromosme is not diploid, the germline mode does not really fit. I read the documentation but found...

NOTCH2NL should be NOTCH2NL**C** in: - https://github.com/Illumina/ExpansionHunter/blob/master/variant_catalog/grch38/variant_catalog.json - https://github.com/Illumina/ExpansionHunter/blob/master/variant_catalog/hg38/variant_catalog.json

Hi Lisle, I found a little bug in your BED file parsing: Header lines without tab are treated as data lines. Thus, they lead to a crash because the second...

MNP handling in version 1.0.9

2

Hi, I have a question about MNP handling in 1.0.9. I created the following minmal test VCF: ``` ##fileformat=VCFv4.2 ##fileDate=20231214 ##source=freeBayes v1.3.6 ##reference=/tmp/local_ngs_data_GRCh38//GRCh38.fa ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT=...

Hi, I just built and installed vcflib 1.0.9 on Ubuntu 20.04 using these commands: ``` git clone https://github.com/vcflib/vcflib.git vcflib-1.0.9 cd vcflib-1.0.9 git checkout v1.0.9 && git submodule update --recursive --init...

Hi, I probably found a bug - or I did not get how to use BAM file indices :) When there is no index file present, we used BamReader::CreateIndex to...

Dragen offers special callers for several medically relevant genes: https://developer.illumina.com/news-updates/dragen-4-2-enhanced-machine-learning-new-targeted-callers-and-more https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/TargetedCalling.htm (enable with --enable-targeted=true) Especially relevant are: - SMN1/2

germline - rare disease ======================= - optimal cohort size - cohort selection - no relatives - only indices? - RNA QC - exons/genes that are lowly/not expressed - validation -...