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Hi Brad,
I am assuming the recall jar uses optimized parameter settings for the variant caller based on bcbio settings. I've been looking at exploring incremental join calling on tumour only samples.…
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Hi Erik
I've been running Seqwish with the output from minimap2 and edyeet for comparison, across multiple chromosomes and also testing with multiple whole genomes.
I've found the PAF files fro…
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GATK is throwing an error because it complains about ReadGroups. This [BioStar](https://www.biostars.org/p/115819) might have some solutions on how to overcome this.
``` java
root@2f68d7ec1b12:/home…
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If a query is performed that requests reads from an area larger than the reference, what is the result?
i.e. Reference is 1000 bp long. Query starts at 900, ends at 1500. Are all the reads overlap…
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Hi,
I want to map short reads to a large gfa graph and get the reads information about which paths mapped to and which postion (nodes id) in the paths. The big gfa graph merges the gfa graphs from…
zwh82 updated
10 months ago
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Make `-Werror=missing-methods` a default.
I would like to gauge the interest/response before making a proposal.
Currently omitting method implementations in type-class instances
is just a warni…
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Hello!
I address you because I want to perform a little experiment using graphs. I would like to make a string graph from several similar reference genomes. Once made, I would like to convert the str…
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We are close to releasing our new pipeline schema which describe input parameters. Through chatting to people at BOSC 🍐 I've become aware of a project called [Bioschemas](https://bioschemas.org) which…
ewels updated
3 years ago
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Hi
While running vg autoindex I get complaints about the sequence length being too long. I had the same problem when running vg gbwt, so I set the buffer size to 1000.
Could the same parameter b…
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Hi, Tanya. Can you please prepare a table that lists…
+ [x] the number of GitHub watchers, stars, and forks for each formula in Homebrew/science that has a GitHub a repo https://github.com/Linuxbre…