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Hi,
Many thanks for making all code and data available. I am very keen to access this file (https://cgl.gi.ucsc.edu/data/giraffe/products/vggiraffe-sv-relkgp-raw.vcf.gz) reflecting the SV calls fro…
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When I install samplot using "conda -c bioconda samplot", it always reports the error: "UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in forma…
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Hi there,
I'm trying to use SURVIVOR to merge matching tumour and normal vcfs generated by sniffles from PromethION data. However, this seems to be erroneously losing variants during the merge. I'v…
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Hi,
I have recently aligned the [CHM13](https://github.com/marbl/CHM13) v1.0 assembly from the T2T consortium to the reference genome GRCh38.p13. I subsequently tried to detect SVs from the CHM13 a…
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Hey Brent,
I'm looking to run Excord on 1kG data from the NYU remap to GRCh38+alt.
Wondering 2 questions:
1. Can Excord work with streamed CRAMs?
2. Roughly how long and how much RAM is neede…
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The SV inspector could offer to add a BAM and VCF track up front to make it easier for people to launch into the breakpoint split view with the tracks that they need loaded already available, so that …
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**Describe the bug**
I am using WSIReader as either transform or SlidingPatchWSIDataset, the resultant maps are mirror flipped always.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to …
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Hi there
I am using ngmlr with some raw nanopore reads and its working fine with "--presets ont", However, my average readlength and coverage is not too great, so I was exploring changes to some pa…
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Hi,
I am using minimap2 to map long ONT reads (up to 400Kbp), and I am finding that the supplementary chaining is producing large rearrangements in the read sequence, flipping strands, and jumping …
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Hi @lh3,
It would be very useful to us to have support in ksw2 for "infix" or "fitting" alignment, where they query aligns within the target, but the precise starting position of the query is not…
rob-p updated
2 years ago