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We had an issue where VCF track builds were being cut short, because those tracks had unexpected chromosomes as an artifact of liftover.
Need to write tests for all tracks, especially those prone t…
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Hello,
I tried to predict high resolution matrix using the [processed file](https://www.dropbox.com/sh/5b5thuk62px5qpk/AAA5n_Mz1maFp3ucTYMYQ7mma/deephic_10kb40kb_c40_s40_b201_nonpool_gm12878.npz?dl…
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Dear Armando,
I am trying to run the analysis with your example data but the script resturns me this error:
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROM…
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I'm working on a Linux based HPC working with private data hence the environment is restrictive (no internet connection); therefore packages must be built from source.
After downloading the file an…
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| Exercise | Description | Completion |
| -------- | ------- | ------- |
| Q1 | `grep.py` completed | Yes |
| | `sys.argv` indexed | Yes |
| | Text file processed | Yes |
| | Newline characters r…
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Gene-set burden tests where the genes span multiple chromosomes are difficult to run because regenie [only supports running on a single genotype file set at a time](https://github.com/rgcgithub/regeni…
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```
PyGEP should support RNCs (random numerical constants) per the GEP book,
2nd ed., ch 5. The way I'll probably do this is by recognizing the '?'
terminal symbol in chromosomes, so one can define a…
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Hello,
I've recently discovered this tool, and want to try it out on a large vcf.
I was wondering, is there any way to get LD analysis + plot across all chromosomes? I have chromosomes 1-18, and i…
siv-n updated
3 years ago
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Hello, I have broken down the human CADD scores file into individual chromosomes and included all the resulting 24 files in the config file to speed up the annotation process, but it doesn't seem to b…
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Hello everyone,
I am conducting research on the Pine Processionary Moth and I want to call variant on the sexual chromosome.
In my data I have males that are homochromatic ZZ and females that are …