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Gold standard benchmarking datasets such as the GIAB/NIST NA12878 and the Illumina Platinum Genomes truth sets provide both a VCF containing the variant records themselves, plus a BED file of "high co…
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### Bugs
- [x] ~~Z-scores not calculated, leading to no samples meeting the threshold. Not sure what the issue is, haven't delved into it deeply.~~
- [X] ~~Output is quite messy and doesn't look qui…
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Dear all,
So I've tried using LDBlockShow on a QTL dataset to visualize the linkage blocks between biallelic SNPs.
I tested to observe the blocks before and after pruning to understand how the pru…
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Hello,
I've noticed that some variants are reported as PRECISE and with a PASS filter but when taking a look at the alignment in the IGV the position reported is wrong in comparison to the actual p…
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Motivated by suggestions from @brentp and Manuel Rivas (https://twitter.com/manuelrivascruz/status/590250919570186240), it is clear that a simple API would be beneficial. In particular, providing a we…
arq5x updated
8 years ago
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Hi dear author,
we want to use and cite your tool in our paper, but we are not so sure about the meaning of these two parameters: maxdist and maxdiff. For example: what is "cluster variant" ? W…
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There's a new, promising method for tumor-only SNV calling:
[Repository](https://github.com/AbbVie-GRC-Methods-Dev/new_normal)
[Manuscript](https://www.nature.com/articles/s41698-022-00340-1)
It …
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Hi,
We are using the -a E option to filter known SNPs based on a VCF file. In this example, the VCF file we are using for input was obtained UCSC, here: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/hu…
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Hi Brent,
I was wondering if you are aware/have an easy way to run SOMALIER but only consider the relatedness when n (the shared number of sites) is higher than a given threshold.
This would be…
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This user is trying to subset all of the variants in their mutant samples that are not in the wild-type sample. The --discordance argument with the wild-type file specified is giving them 0 variants b…