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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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Hi, I obtain a `.pop_like.txt` with all nan values after assignment and couldn't figure out what would be the problem.
I use a reference (breeding) population: 60 individuals from 12 populations 4…
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Hi,
I am encountering an issue similar to what was described earlier (#3429) in gatk-4.0.7.0, in which I find that the GenomicsDBImport combines gVCFs but leaves the majority of variants out of the …
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Hi guys,
could you please consider aligning your VCF output to the [VCF spec](http://samtools.github.io/hts-specs/VCFv4.1.pdf), which requires that PL field contains ` likelihoods for all possible …
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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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Hello,
I am new to using WASP and am trying to phase my genotype data using SHAPEIT. I used the shapeit -convert command but only get the impute2_haps.gz file equivalent and cannot figure out how t…
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I am genotyping 10 individuals with _mpileup_ and _call_ commands and I am getting some strange results.
I am using this code:
bcftools mpileup --skip-indels --annotate FORMAT/AD,FORMAT/DP,INFO…
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Dear Jonas,
I read the paper and I've to congratulate, because is really interesting! I contact to you because I'm interested to use BayesTyper to genotype my samples. I've 808 samples (at 30X) whi…
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Hi
Version 0.8.1 of Platypus generates the following header lines:
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
##FORMAT=
I agree that according to VCF specs, the number entry has t…