-
In the Step 5 - Single Nucleotide Variant calling cell by cell,
Could you tell me what the role of the SNPs descriptor file is?
Does it is the SNP calling results at the overall sample level, or is…
-
Hi, first, thank you for interesting tool to use in single cell
I have a question about SNV output(chr*.putativeSNVs.csv).
When I put input bam file, bam file have 8923 unique cell barcodes,
bu…
-
Ran on sample using command:
```
# ont version code
spectre CNVCaller \
--bin-size 1000 \
--threshhold-quantile 10 \
--dist-proportion 0.3 \
--coverage input-files/ \
--sample-id…
-
In omicron SC2 sequences there is difficult area (3 bp deletion - 8 bp - 9 bp insertion). Typical aligners produce more soft clips than insertions.
 PR #116 & turning it into a feature request for discussion.
## Goal
Rather than printing `missense_snv_col` in plots, print `Missense SNV Count / MB` or `Missense SNV Count`, depe…
-
Apparently we're not reading these in, though we do read in the protein's annotated modified residues. It may or may not be a good idea to read in all SNVs, etc. but maybe we should provide options to…
-
## Short description of the problem
`anvi-script-visualize-split-coverages` is unable to produce a pdf when given SNV data.
## anvi'o version
```
$ anvi-self-test --version
Anvi'o .......…
-
Hi @hannespetur,
Sorry I might have missed this somewhere. Does Graphtyper perform SNV discovery from PacBio or Nanopore data or is this something still under development?
Thank you
Kind reg…
-
This is an idea by @johanneskoester to speed up single nucleotide variant calling:
Currently, caching of reads in a window around candidate variant sites is optimised for indel calling. As for thes…