hap.py
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Illumina
Haplotype VCF comparison tools
I get the following error message: Log: ``` 2019-11-19 17:31:03,363 ERROR [stderr] Segmentation fault (core dumped) 2019-11-19 17:31:03,483 ERROR Command 'quantify /tmp/hap.py.result.IJlnIM.vcf.gz -o /mnt/projects/external/promethion/vc_comparison_NA12878/out/promethion.roc.tsv -r /mnt/projects/external/promethion/reference_genomes/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --threads 5 --output-vtc 0...
Hi,Peter I want to compare two VCF file using hap.py, So I try to test hap.py as document described, ,But I got serval error messages like below,Can you give me...
Hi there, I'm trying to compare two vcfs and getting the following.. ``` [W] overlapping records at chr1:26686335 for sample 0 [W] Variants that overlap on the reference allele: 247...
Hello! The option `--no-rebuild-external` doesn't exist in the `install.py` script but is mentioned in the `README.md`.
Hello! This step doesn't work now: https://github.com/Illumina/hap.py/blob/dac84d9c5aa50ee805de2edb7af10e6e1a58721a/Dockerfile#L22 I suggest: ``` RUN add-apt-repository -y ppa:openjdk-r/ppa \ && apt-get update \ && apt-get --yes --no-install-recommends install \ openjdk-8-jdk ```
Hi, I am comparing two vcf file, and get the following errors: ``` [W] overlapping records at 1:6799149 for sample 0 [W] Variants that overlap on the reference allele: 1346...
Hi Peter, I'm running hap.py to compare the F1-score of different variant callers for exome data using the GIAB truth set as reference. In order to check how strong the...
Hi i am getting this error for this sample. The error only occurs with this sample NA24385 by using bwa alignment. I did run analysis for the same sample by...
Hi, I could not find in the documentation of hap.py how TS_boundary and TS_contained regions are assigned to various variant locations. Could you please give an explanation to that, and...
