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Dear all,
I'm here for the first time in the community and have been trying for some time to obtain a pangenome to use as a reference for mapping short reads using `vg giraffe` and subsequent varia…
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HaplotypeCaller expends massive effort to generate a set of local candidate haplotypes along with their read likelihoods. After that, however, it throws away the haplotypes, using them _only_ for the…
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Input: PacBio long read, HiC and Illumina short read data
Assembly: Canu v2.1.1 and then run my assembly through purgeHaplotigs
Variants: FreeBayes
I process HiC and PacBio files as recommended …
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- Need to formulate inference algorithm
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A high-level overview of major new features in VRS 2.0 would help with orientation.
Create documentation for the following major new features:
- [ ] Descriptive metadata
- [x] GA4GH Keys
- [x] S…
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I have found a rather amusing edge case in the haplotype trimming code where by dumb unluck we we threw away all the haplotypes in an assembly region. At this site we have discovered variants from the…
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Hello, I ran "selscan --xpehh --vcf vcf1_Chr1.gz --vcf-ref vcf2_Chr2.gz --pmap --out outfile", but no files were generated.
The result of the operation is:
selscan v1.3.0
Opening vcf1_Chr1.gz...
L…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…
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`chr18 28481424 Minda_60 N ]chrX:95812868]N . PASS SVLEN=-1;SVTYPE=BND;SUPP_VEC=PB_severus_BND2976_2,PB_ID_40283_2,ONT_severus_BND3369_2,ONT_ID_69368_2,PB_r_192_1,ONT_r_114_1,ILL_gridss260fb_8331h,ILL…
jzook updated
3 weeks ago