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Numbat has [Using Existing CNV Calls](https://kharchenkolab.github.io/numbat/articles/numbat.html#using-existing-cnv-calls) for borrowing information from sample-matched whole genome sequencing. Such …
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User story:
As a user, I want easy access to browse all studies in the Catalog, and to be able to see GxE studies only. I want this to be presented on a separate page, https://www.ebi.ac.uk/gwas/stud…
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Hi,
Thank you for developing a useful tool to merge SVs from sequencing datasets.
Currently, I am using HiFi data to call SVs using different callers: sniffles, cuteSV, pbsv, and svim for the Hi…
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Hello,
Is the WASP mapping pipeline suitable/recommended to be used on WGS data? I have followed some suggestions here to split some of the steps by chromosome since the files are large. However, f…
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In addition to cfDNA, whether the ichorCNA can be used for gDNA?
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Hi all,
I am new to the field and I'd like to verify my variant calling pipeline using latest CHM13 as reference. I have the HG002v1.1.fasta here and I got the truth set v1.1.vcf from NIST.
> (ht…
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Hello!
First of all, thank you for sharing IsoLamp with us.
I see that IsoLamp was created for the targeted sequencing, but I have a small newbie question. I was wondering if it would be possibl…
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This is something I've been doing off-bcbio for quite a while and I think it would be worthwhile to streamline. I would like to use this issue to collect information on how people have been doing thei…
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Hello,
I have some whole-genome sequencing BAM files of T-cell leukaemia. I was wondering how I can modify IgCaller to call T-cell receptor (TCR) rearrangements. Some guidance on how I can modify t…
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I thnk that I could model non-methylated Cs as C->T SNPs and Gs as G->A SNPs , but the VCF will be *VERY* large.
Since methylation sequencing is directional, I'll also have to do a second simulatio…