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Hi,
I've been trying to compare some variant calling methods to use on mitochondria NGS data.
I've seen that you test your pipeline with HG00119 and I was wondering if you had curated a set of hig…
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I have already sequenced a batch of yeast data and would like to use Haplocheck to detect contamination in the WGS data. I note that the examples mentioned in _Contamination detection in sequencing st…
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I'm trying to layout what the restrictions on graph imposed by jVCF are. I'll list criteria and what may happen if they are not met
Possibilities:
* Graph is directed
If graph is not directed, …
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Hello,
I am wondering why certain variants in the *annotation.csv file are not annotated with a heteroplasmic fraction. The same variants ARE annotated with a heteroplasmic fraction in the vcf. Fo…
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Re: Iain's comment in issue #23 (as it concerns the faulty promotion of positive ambiguous calls based on our rule engine) -- "The best solution may be to allow the user to provide an input set of pri…
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Dear author,
I tried to train my databse with train.py, but I got the error below, any suggestion? thanks!
regards
wang
python train.py /home/predict_y_haplogroup/database.csv
0.828828828828828…
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**Recipes**
- [x] fastqc
- [x] bwa_mem
- [x] picardtools_mergesamfiles
- [x] markduplicates
- [x] gatk_baserecalibration
- [x] chanjo_sexcheck
- [x] samtools_subsample_mt
- [x] tiddit_coverage…
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Hello!
Would it be possible to add T2T to Yleaf positions and support for T2T-CHM13v2.0 reference?
Thanks!
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When trying to annotate with Haplogrep2, it complains because INFO contains whitespace from gnomAD. Source gnomAD VCF already contains this, so I need to fix it at the Dockerfile.
Exception is as …