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Hello! Is it possible to use tensorqtl to perform QTL analyses with _genotype likelihoods_ derived from low-coverage whole genome sequencing data, instead of hard-called genotypes?
Thanks for an…
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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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Good evening,
`ngsPool` provides `poolSFS.R`, a script which estimates a one dimensional SFS from the `SAF.GZ` output file. Is it possible for other software to read pairs of "sample allele frequen…
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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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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 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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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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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…
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Hello,
I’ve tried with both .bam and .mpileup files but keep getting the following error:
python3.5 Genotype_Likelihoods.py PileupList.txt
Seed is not set.
Default ploidy levels to be tested in…