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Hello,
My name is Lauren, I am currently trying to use simuPOP, but have have not been able to resolve an issue on my own.
I have genotyped ~3000 SNPs in 20 individuals from a small population of…
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I have another project! The genome size is about 1.7Gb. We have sequenced it about 60X with RSII. The L50 with default parameters is about 300Kb. I don't satisfy it! Someone achieved the L50 of 1Mb. S…
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Just need to expose `InbreedingCombiner` in expr language. Needed for GnomAD QC.
Related issue: https://github.com/hail-is/hail/issues/501
cseed updated
8 years ago
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Hi,
this seems could be a bug in vcftools-0.1.14 not removing entries with INFO field being INDEL. Seems the annotation stems from bcftools-1.2 which did the initial SNP callling.
Anyway, I am…
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Hope this helps!
The VCF below throws an error. It has a single sample. Trigger the error by running:
```
from cyvcf2 import VCF
v = VCF("in.vcf")
for record in v:
record.gt_bases()
``…
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Dear Thierry,
I am using your package to input a large amount of data to Colony. Our package is the unique way to pass data from stack to colony.
1- First, i use a awk script to filtred out lo…
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Tested with the fresh profile of [Pale Moon 27.0.3 x64][1]: **userscript** no longer works.
Rolling back to [1.7.3](https://github.com/ParticleCore/Particle/archive/1.7.3.zip) until something good ha…
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Hi ANGSD team,
I have trouble making sense of the output from `-HWE_pval`. I am trying to filter out loci with negative F as a way to remove likely paralogs. I have run the following command on BAM…
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HI
I tried using `vk calc` to analyze a GATK produced VCF and got an error:
```python
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/vcfkit/calc.py", line 1…
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Using the latest vcf2db
Codon field (codon_change) is blank. I'm using VEP to annotate consequences.
```
$ gemini query -q 'select chrom, start, end, codon_change, aa_change from variants WHER…