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dear all,
Im having problems to run snippy 4.6.0
When I --check dependencies, I receive the following message:
[11:09:57] This is snippy 4.6.0
[11:09:57] Written by Torsten Seemann
[11:09…
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Hi:
my data , F1 , tetraploid , 7 chromosomes , NGS data , BWA and GATK haplotype .
there is not 7 linkage groups , just like one .
Your paper used the SNP array data ,and said "Dosage estimatio…
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I constructed vg graph using freebayes VCF and why we detect snarls with node_id in backward direction?
I would expect everything to be forward, is it not?
```
Example 1:
{"type": 1, "start": {"…
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I removed "-I -X -u " from lines 450 and 456 to allow freebayes to report non-indel variants (SNPs, MNPs and Complex variants) in addition to indels. Could I trust the reported variants? Is there any …
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Input: PacBio long read, HiC and Illumina short read data
Assembly: Canu v2.1.1 and then run my assembly through purgeHaplotigs
Variants: FreeBayes
I process HiC and PacBio files as recommended …
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@ekg
Hi Erik,
As you suggested, I tried different parameter values for PacBio data, something similar to BWA mem.
When I used
```
vg map -k 17 -W 40 -r 10 -q 2 -z 1 -o 1 -y 1 -x yeast.illu…
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@mari-ga and @wxicu please modify the section on minimum required inputs following this:
The hashing and genetic mode are two independent workflows, and the rescue mode allows to perform joint demu…
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A lot of our errors look like this:
But when we go to tview, we see that the problem. Th…
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Hi,
I'm maintaining this code for the Debian distribution as a predependency for FreeBayes. For the maintenance in Debian it would help a lot if you would consider tagging releases as distributable …
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We need to use the same gene region when switching between refseq and gencode to avoid different scales as illustrated: