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I have perhaps an unusual use case. I am using whole genome methylation data from multiple closely related vertebrates. In order to compare apples-to-apples, I need a common coordinate system so I lif…
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Hello Eoghan and team,
After multiple rounds of nanopore sequencing we have reached to 50-60 Gbases data for each sample. Pore-C run results in ~250 million contacts each. However downstream proces…
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Hi:
I'm looking at some 30x ONP human genome data and seeing that sniffles appears to overcall variants as translocations (BND) when in fact they contain a duplication. These BND variants are being f…
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The breakpoint split view is a good first step, but we need more powerful tools to understand more complex rearrangement events.
Figure idea:
https://www.nature.com/articles/s41586-019-1913-9/fi…
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While most human population genomics datasets are now able to achieve >30x sequencing coverage on the regular, for a lot of non-model organism studies its becoming more popular to instead use low-cove…
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Hi,
I would like to test your tool. How can create the two input files. I have the results from a cellranger run, i.e. bam, fastq, and count matrix.
Thx
Bernd
baj12 updated
2 years ago
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How does Varscan (v2.4.3) determine that two consecutive SNVs are part of the same event and call the variants as a MNV?
I have multiple examples where BAM files (which have gone through differing …
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I have installed snippy in mac OX intel 64 using brew. No issues checking dependencies, except that the bcftools version required was 1.7 and the one installed was 1.16. I installed version 1.7 from s…
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I am interested in calculating copy number values for each sample in set of normal (blood) samples. I read the Germline Analysis section, which recommended the call command. But, the call module requi…
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Hello V-pipe team,
Thanks for the wonderful tool.
My v-pipe works fine, however I am getting this warning (Warning: All reads at position 4045 in the same reverse orientation ?) for number of positi…