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Hi
What would be the best way to output active regions from GATK4 HaplotypeCaller?
In GATK 3.x, an option `--activeRegionOut ` could be used to write active regions in a TSV file. However, I am …
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When looking at the help of the mpileup subcommand:
```
$ /software/samtools/samtools-git/samtools mpileup
Usage: samtools mpileup [options] in1.bam [in2.bam [...]]
Input options:
-6 …
ghuls updated
7 years ago
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Hi there,
I'm looking to merge some VCF files but when I try I get the following error message.
"Incorrect number of GL fields (3) at chr1:12719, cannot merge."
Input command :
bcftools mer…
eddip updated
7 years ago
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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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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/78) by Tobias Marschall (Bitbucket: [tobiasmarschall](https://bitbucket.org/tobiasmarschall), GitHub: [tobiasmarschall](https://github…
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What is the difference between a SAM and BAM filetype. Which one could you use to find variants (ie SNPs) and what would an example command look like?
What is one means by which the text indicates …
sr320 updated
7 years ago
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The gene `SETD5` is associated with `Mental retardation, autosomal dominant 23`. If I use `intellectual disability`/ `HP:0001249` the phenotype score is 0 (PhenIX and hiPHIVE). The strange thing is th…
visze updated
7 years ago
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When I do `bcftools view -i 'MQRankSum="."'`, then this record is printed:
10 67402 . C A 52.98 . ABHom=1;AC=2;AF=1;AN=2;BaseCounts=2,0,0,0;DP=2;Dels=0;ExcessHet=3.0103;FS=0;GC=41.65;HaplotypeS…
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(given a source and sink, genotype paths)
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Issue: cross reads from X to Y in PAR regions lead to problematic sex inferences. In a cohort of 112 sex annotated samples, a single XX -> XY misclassification was noticed, which was identified to be …