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Hi,
What is the maximum size of variants (e.g. deletion) VV can handle?
This
https://rest.variantvalidator.org:443/variantvalidator/hg19/chr1%3Ag.216210459_216266638del/all
raises an error for exa…
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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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Based on a survey of the variant types used in CIViC as a starting point:
- SNVs (single nucleotide variants). e.g. `R175H`
- MNVs (e.g. dinucleotide variants). e.g. `VHL c.364_365GC>AT`
- Insert…
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Hi
I have been using SAIGE-GENE+ (specifically the GBAT test) extensively for the past couple of months. I now want to run the GBAT analysis with my own groupFiles. I am generating these groupFiles…
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Hi ..
I have Nanopore cdna reads and tried variant calling for this data. One set was analysis with reads without error correction where i see a lot of variants (~500). Further after doing error corr…
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Hello @Cloufield
I'm getting a weird error when performing a liftover that I can't explain.
Gwaslab is unable to lift 4 SNPs, while when I use the [liftover library](https://github.com/jeremymcrae/l…
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Problem reported by Siim, similar to #51, except that the order of `` `chr` and `chr` `` is reverted.
I need to run the LDPred2 separately on all chromosomes (can add all the sumstats as final st…
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Use cases:
- Storage (long-term)
- Storage (short-term)
- Streaming
- Random access
- By class
- By genomic range
Metrics:
- Compression ratio
- Compression speed
- Decompression speed…
voges updated
3 years ago
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The joint caller should optionally output a csv file that gives for pairs A, B of variants (both germline and somatic) at each sample:
- total number of fragments (i.e. reads or mates of reads) overla…
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It needs filling in.
@SarahKit can write content?
drj11 updated
7 years ago