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Hi
I'm currently constructing a pangenome from 20 varieties of the same species. The pan-transcriptome is also being generated, with a transcriptome for each individual across different tissues. Re…
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Hi
I've noticed with the more recent updates that a few parameters have changed their default values, namely these values:
max_path_jump=100 (-j)
max_edge_jump=0 (-e)
block_id_min=0 (-I)
block_…
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As the title says. The coding of null/missing genotypes as simply '.' is causing me headaches downstream. I'm even setting --ploidy explicitly.
It is entirely possible I'm just missing something obv…
travc updated
3 years ago
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Hi team,
I have installed gLiveView.sh as a standalone script alongside a testnet stake pool that was not built with prereqs.sh, and am having technical difficulties.
## Problem
My fully up to …
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Hi @ekg ,
I am building a pipeline using freebayes to detect somatic mutation in tumor-only amplicon sequencing. I have been using -F 0.03 to detect variants with low-frequency. However, I have bee…
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Thanks for freebayes. I think it is a great variant caller. Meanwhile:
Modern pipelines (CWL, Arvados, Galaxy) are working towards reproducible analysis. Ideally, on the same set of inputs, the outpu…
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I've encountered a case of an adjacent indel and SNP that were unable to be picked apart by vcfallelicprimitives. The variant is an T insertion into a T homopolymer run and an A->T SNP at the end of t…
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Hey,
I am currently working on a fully portable pipeline and one of the streps is docker/singularity.
I built a docker container with the precompiled binary and it starts (the help can be reques…
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Freebayes crashes with error message:
> new allele qualities not == in length to sequence: Sx8drs-SAMPLE:C38WVACXX_1:8:2116:1266365:0:null:81:81:10267:-:NTNAACNCAAAACCNAATCCAACCCNTNCCCCTCCACNAANNNA…
mrtnb updated
3 years ago
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Hi
I have problem with vcf-files, generated by freebayes, and specifically phased variants.
If I run vcf-validator I get the following output:
> column SAMPLE-1 at chr2:113982039 .. FORMAT ta…
Smeds updated
3 years ago