adVNTR

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When --haploid option is given, the output format should be changed accordingly.

Jong-hun-Park

sqlite3.OperationalError: disk I/O error

2

Hi Mehrdad, I'm trying to run advntr on some PacBio reads mapped to hg38 and I'm using the hg38 models (hg38_selected_VNTRs_Illumina.db) however I get a `sqlite3.OperationalError` when running with the...

Parsoa

Hi there, adVNTR will not work unless the h5py version is changed to 2.10.0. Perhaps the conda environment could be updated to reflect this?

hevmarriott

Issues running advntr genotype

9

Hi, After installing the package, I'm having difficulty getting the genotype command to run on some pacbio bam files. Running the following; advntr genotype -p -a NA07019_SC034768.bam --update -m vntr_data/hg19_VNTRs.db...

aob93

OSError: [Errno 24] Too many open files

3

Hi, apparently I have a multiprocess error when running adVNTR ; the command : advntr genotype --alignment_file $bam --working_directory $advntrDir/$bam_name --vntr_id 25561 --pacbio --frameshift -m ../hg19_selected_VNTRs_Pacbio.db -t $Ncpu the error...

nbargues

trained VNTR models for Nanopore data

3

Hi, when I download vntr_data_recommended_loci.zip , there are two files ( illumina and pacbio ). If I have Nanopore data, can I choose the pacbio file or do you have...

nbargues

For VNTRs on chrY, we can first check if we can call homozygous calls for VNTRs on chrY and output the haplotype only if the call is confident.

Jong-hun-Park

cannot create my custom database

3

hi, i installed the latest version of adVNTR （v1.32） using miniconda: conda install -c bioconda advntr, and erverything is well but i cannot add (create) a new .db ohh! i...

jxlabWzZ

Suggested by Nick in #17

mehrdadbakhtiari

- `hg19_chromosomes/CombinedHG19_Reference.fa` is hard-coded in many places (ex. `src/reference_vntr.py`) - `chr9.fasta` is hard-coded in a supplementary script - chromosome names are defined in `settings.py`, and not using a sequence dictionary...

nh13