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Hello,
I'm trying to do a hybrid polish of a large genome with Illumina and PacBio. Looking at the current rate using 20 threads, it will take me 3 months to complete the polishing. Is there a diff…
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Hello,
I have been trying to genotype structural variants from a graph made with minigraph-cactus, by mapping short reads with vg giraffe, then using vg pack and vg call to get a vcf. This runs wit…
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When build index with large genome, I got this message:
```bash
Could not allocate space for a joined string of 1074914909166 elements.
Switching to a packed string representation.
Total time for …
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Our minimum viable test set should be small enough to allow local development but complete (and probably large enough) to do some actually meaningful work. Thought is to perhaps keep just a large coll…
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Hi, @lrauschning
I tried `msyd` with 279 A.thaliana genomes, but the core synteny region is small. For example, Chr1 only has several regions beginning only in the Chr1:1-200000 and Chr1:2700000-3…
baozg updated
3 months ago
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FYI: estimated genome size is 2.2 Gb and coverage of illumina ~ 70X and PacBio coverage: ~14X
Getting memory allocation error below (using MaSuRCA v3.2.6) :
terminate called after throwing an…
nm100 updated
2 years ago
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Hi, I've downloaded gnomad211_genome.txt and gnomad211_genome.txt.idx from annovar and put it into the humandb folder. How can I enable InterVar to annotate variants based on gnomad211_genome rather t…
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When the large cohort pipeline is run, default and input config files are merged together to form one, combined config file. If duplicate entries are listed, the entry in the last config file takes pr…
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Hello,
I am trying to mutate a rather large genome, here is the command:
python ~/bamsurgeon/bin/addsnv.py -v input_mutations.bed -f realvariants_Ayumu.sorted.golden.newheader.bam -r panTro6.auto…
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Hello everyone!
bcbio1.2.9 is out - thanks everyone who contributed to testing and bug fixing during the last month!
We were lucky enough to catch openssl1.1.1 > 3.0 upgrade (Sept 2021) which is…