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### Description of the bug
Joint germline genotyping completes actual genotyping, but fails at TSV count vcftools step
### Command used and terminal output
Command:
nextflow run nf-core/…
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Hi
I am thinking about trying the option --genfile. As of my 7500 samples 50 of them have a sequencing coverage of >x15.
I was thinking of taking the file from --outputInputInVCFFormat = TRUE.…
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Hi, I'm getting a segfault similar to issue #92, where GLIMPSE_phase (v1.1.1) crashes during or after finalization. This only occurs with haploid data (in fact if I don't provide a `--samples-file` an…
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In bd46c4e8f09bce6c5837857a2d88d458aff71d70 I've committed a small test example to understand why we always seem to get equiprobable posteriors (0.333 0.333 0.333). Varying the flanking_snps option to…
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## Problem
Match prediction is an intensive process.
It is also deterministic: same input will result in same output.
Thus caching calculations could save on computation.
Input for match prediction:
…
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Hi, I'm getting strange genotype calls and then a crash with my GATK VCF.
The zygosity call is strange, but the VCF passes validation.
I've reduced it down to a few lines (VCF at bottom of issue…
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I have some phred scaled GLs stored in a BCF with format header:
```
##FORMAT=
```
I have managed to get a pointer to a `bcf_fmt_t` struct for these GLs as described in the header file `htslib/vcf.h…
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I'm trying to understand what the added fields T, E, GO, and GN are in the vcf output by `consensus.py` (`cluster_genotypes.vcf`) I don't see these tags in the output from freebayes, and that they're …
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In `GEMMA`, bgen support was added in [PR](https://github.com/genetics-statistics/GEMMA/commit/35546b026899306f1bd212cee472baaa6dc393de).
However, there are no tests to validate the code so that I …
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Hi,
Can RUTH handle chromosome X? There isn't a mention of it in the manuscript, but the program accepts parameters for sex chromosomes. When I try to load a BCF file containing X-chromosome SNPs, …