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I'm curious to hear people's opinions regarding whether or not a variant can or should encompass multiple alt alleles. It seems that version 0.5 of the variants.avdl supports multiple alts per varian…
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If there are snp-genotyping results for a project, if should be possible to add those into the analysis. However, these might not always be available, so this needs to be a optional step.
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Hello,
I was rellay happy to see ngstool working in combnation wit ANGSD. I made my first steps with ANGSt recently , and tested ngsF. I am working n yeast and I was interested in estimating selfing …
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- When I tried to convert the 1000 genomes data into plink format with `bcftools -Ob` and `--bcf` option, I found out all haploid calls on chr23 (chrX: Non-PAR) region are ignored (ex.1).
- With `bcf…
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I'm doing basic SNP genotyping with freebayes using a target bed file, but it is skipping the first entry in that file. I can add a dummy entry as a workaround, but that is hackish.
It does attempt …
travc updated
9 years ago
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Hi!
It seems I am running into a common problem with Headers but can't figure out how to solve it.
I am using PyVCF-0.6.7-py2.7-macosx-10.5-x86_64 and try to iterate records on a VCF file and get thi…
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Possible bug: in short the snp '5504' is pruned out but should not.
```
plink --bfile g10 --indep-pairwise 10 1 0.6
(~ window of 10 snps, step by 1, min R2=0.6)
cat plink.prune.out
5299
5329
5364
54…
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Hello,
On my dataset (available upon request):
plink --bfile pair485_486 --ld 485 486
```
PLINK v1.90b2p 64-bit (22 May 2014) https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, C…
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Related to #102
We should use counter_caches where we count things to improve speed, for example on the genotypes-index
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Hi Brad,
I am trying to use bcbio-nextgen to analysis whole-exome seq data. However, an error stopped the process, the detailed info is:
[2014-09-02 22:42] Finalizing variant calls: C3, freebayes
[2…