-
# nf-core/sarek feature request
## Is your feature request related to a problem? Please describe
Typical effect prediction (SNPEff, VEP) will not take into consideration variants "in phase", i.e…
-
We attempted to correct sequencing errors in HiFi data using alternative methods without utilizing hifiasm's error correction feature. Hence, we attempted to disable hifiasm's error correction funct…
-
Dear @alexdobin,
I've noticed that reads that are assigned to haplotype 2 by STAR diploid are not processed in the same way as haplotype 1 reads by STARsolo. For instance, I am fairly confident tha…
-
After running CRISPRme version 2.1.5 on spacer `sc1617.txt` (`"CTAACAGTTGCTTTTATCACNNN"`) using the tutorial provided scripts, we are observed instances where multiple SNPs are being reported for the …
-
**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
zwh82 updated
2 weeks ago
-
@nspope had a great idea for a tsinfer-like method to identify mispolarised ancestral states. This could form the basis of a comprehensive recombination-aware ancestral state polariser. Note that exis…
-
Hi Prof. Li and Haoyu,
As described in the tile, I am curious about what's your opinion about this process of assembling an allopolyploid genome, such as strawberry.
I think maybe we should use …
-
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…
-
* [ ] Attempt to "ramp" the start of the target region by decreasing -s automatically
* [ ] Minimal marginal aware reweighting
* [ ] Reconsider approach for minimal reweighting
* [ ] Alternative va…
-
## Feature Request
**Some background**
- GRCh38 contains ALT contigs that represent alternate haplotypes to corresponding regions in the primary assembly. We use ALT contigs to represent those hap…