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Am using htsjdk 2.9.1, trying to index a 4gb VCF file, via IndexFactory.createLinearIndex()
It crashes on out of memory. This was somewhat surprising as the indexing is done via iteration on the inpu…
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Currently we compare peptide sequences against a reference proteome from Ensembl.
It would be more correct to create a proteome that incorporated SNPs that impact protein sequence and then look f…
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Issue seems to due to VM running out of disk space. From a MergeVCF log:
```
[Thu Jun 25 08:23:53 UTC 2020] picard.vcf.MergeVcfs done. Elapsed time: 89.52 minutes.
Runtime.totalMemory()=202729062…
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Hi!
I used vg chunk to extract subgraphs from a pan-genome graph and then used vg deconstruct to obtain VCF files for both the pan-genome graph and the subgraph. However, I noticed that the VCF fi…
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Is it possible to merge VCF headers to combine records from different files? I'am trying to do something like this
```rust
let mut out_header = Header::new();
for record in reader.header().header…
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Are genomic positions in sgkit 0-based or 1-based? We should decide and document the coordinate system conventions that sgkit uses.
[Please correct any mistakes I've made below!]
When reading VC…
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Hi,
I was trying to use both surpyvor and truvari for SV benchmarking. Truvari has an option to input a bed file to limit comparison to only high confidence bed regions. Is it possible to have that…
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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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### 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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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…