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Hi,
First, thanks for developing updog!
I'd like to use the results from updog with another software, Entropy (https://bitbucket.org/buerklelab/mixedploidy-entropy/), which needs phred-scaled ge…
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While most human population genomics datasets are now able to achieve >30x sequencing coverage on the regular, for a lot of non-model organism studies its becoming more popular to instead use low-cove…
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This might be a "next release" sort of goal, as it's beyond what we plan for the paper but would nevetheless be helpful.
At the moment we are only calling SNV mutations because that's what our DM mo…
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When processing a BCF file, we can either calculate our own genotype likelihoods from the AD fields, or use the values calculated in a GL or PL field. Creating an option to dng-call and dng-loglike w…
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Hi,
I'm trying to run Bgc-hm on genotype likelihoods and I think to have formatted the data according to the required input format (see image for P0 example), however when I start to run est_p…
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Hi Armando,
I'd like to try GONe on a low coverage dataset. I have LD estimates already generated using another program that uses genotype likelihoods for LD estimation from low coverage data. Is the…
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Hi guys,
currently, `PL` field in the VCF output of SCcaller is defined as follows:
```
##FORMAT=
```
whereas according to [VCF4.3 spec](http://samtools.github.io/hts-specs/VCFv4.3.pdf) it …
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Hi,
I would like to use 'distAngsd-geno' for a large isolation-by-distance analysis in lemurs. I am primarily working with genotype likelihoods estimated with ANGSD. Because I was not sure what in…
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Example:
This line parses normally:
##FORMAT=
whereas this line:
##FORMAT=
results in this error:
Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description=…
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A small minority of samples (so far 1 in `wes_repo`) repeatedly error out with the following:
```
Traceback (most recent call last):
File "/usr/bin/conpair/scripts/verify_concordances.py", line 3…