Support for QIAGEN CLC genomics workbench vcf
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Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 20/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reproducing the supplied VCF record with bcftools and reviewing how existing genotype and VCF handling treats the GT:AD fields. Done means determining whether the QIAGEN reference-overlap representation is supported and, if not, defining the required translation behavior.
Written by the indexing model from the issue text.
Description
Dear Samtools team, do you support VCFs exported from QIAGEN CLC genomics workbench? QIAGEN CLC genomics workbench is able to represent complex overlapping variants in recommended reference overlap format (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/1203/index.php?manual=Complex_variant_representations_VCF_reference_overlap.html#fig:vcfoption)
The format is helpful for representing complex regions of the human genome. However, I can't seem to find a function that interprets this VCF format. So I am wondering if it's currently supported or will be supported in the future?
For example, for the first Reference overlap and depth estimate VCF entry in their Figure 6.32
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testsample
1 4 . GG TT 200.00 . . GT:AD:DP 0/0/1:6,4:10
Can bcftools translate the GT:AD to specific genotype calls?
Thanks
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
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