Comments (3)
What is BND?
from paragraph.
It's a "Break-end" -- something that can't be classified as a DEL/DUP/etc. See the VCF spec for the full gory details. I just want to know if it will ignore those or if I must remove them from the VCF.
from paragraph.
You can genotype each sample separately. Or you can split the VCF into chunks and feed them into Paragraph separately. Results won't be different.
BND is not supported in v2.2. They need to be removed from the input VCF.
It is hard to decide what kind of variant a BND is. Instead of providing unconfident information, we prefer not supporting it for now.
from paragraph.
Related Issues (20)
- Can paragraph be used for indel from 2 bp to 30 bp? HOT 1
- ValueError: Invalid VariantRecord. Number of samples does not match header HOT 2
- Error with idxdepth: "Assertion failed: _impl->header_contig_map.count(chr) != 0" HOT 1
- Missing key SEQ for <INS> HOT 6
- --vcf-split option with no description
- subprocess.CalledProcessError HOT 2
- grmpy error: [E::cram_itr_query]
- index file
- How to merge multi-samples SVs and obtain breakpoints for genotyping a population
- no BGZF EOF marker
- Install paragraph
- Stop using Werror and Wall
- Genotyping for SNP
- idxdepth regex option not working
- Problem starting the script multigrmpy.py HOT 2
- Error when working with `--ins-info-key` HOT 1
- Add support for VCFv4.2 breakend notation
- Issue's with Native Build and Boost
- Format error in vcf line: HOT 3
- [BUG] Error adding alt from insertion sequence representing a duplication
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from paragraph.