hap.py
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Illumina
Haplotype VCF comparison tools
Hi, Both the provided `Dockerfile` and `Dockerfile.centos6` fail to build for me. The first results in the following error: ``` => [ 9/15] RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && tar xzf apache-ant-1.9.7-bin.tar.gz...
https://github.com/Illumina/hap.py/blob/79de3c780cd5aa5a7cb7ab93cbd65643fafbeddf/src/c%2B%2B/lib/align/RefVar.cpp#L339 The `ref` here is supposed to be the extracted sequence itself; `chr` is the contig name and I think what was really meant to be printed.
I've recently released `vcfdist` as an alternative comparison engine to `vcfeval` or `xcmp`. In summary, it benefits from standardizing variant representations, requiring local (but not global) phasing of variants, and...
my cmd: docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/hap.py gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/gatk_4.1.8.1/Penaeus_monodon_SRR12180364.vcf.gz gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/Penaeus_monodon_SRR12180364.vcf.gz -r gtx_reference_data/reference/Penaeus_monodon/bwa-index/GCF_015228065.1_NSTDA_Pmon_1_genomic.fna -o Penaeus_monodon_SRR12180364_gatk-4.1.8.1 --threads 10 --engine vcfeval error log: [W] overlapping records at NC_051386.1:468540 for...
Hello, I'm interested in looking at the variants that hap.py calls as query false positives and truth false negatives. To do this I am parsing the vcf that hap.py writes...
When I run hap.py with an already reduced TRUTH_VCF and QUERY_VCF, I get the following error: ``` python /projects/xm41/tools/hap/hap.py-build/bin/hap.py joint.gatk.vqsr.pass.FORMATrm.chr12:20723743-20766328.vcf.gz joint.deepv.FORMATrm.chr12:20723743-2076 6328.vcf.gz -f /projects/xm41/robert/compDeepVGATK/HG001_GRCh38_1_22_v4.2.1_benchmark_HC.bed.gz -r /scratch/xm41/hg38_resources/resources_broad_hg38_v0_Homo_ sapiens_assembly38.fasta -o chr12.19061524-21472881.FORMATrm.GATKts_DEEPV [I]...
I have found this line in the output 21 44480616 . G A . . BS=44480616;Regions=CONF,TS_contained GT:BD:BK:QQ:BI:BVT:BLT 1|0:FN:am:.:ti:SNP:het 1/1:FP:am:564.05:ti:SNP:homalt What this really means? Is this a mismatch because of this...
Dear hap.py developer team, I have a question regarding the output of _som.py_. - **Question:** I ran som.py (v0.3.15) using a short variants callset and a ground truth set. The...
Hello, I followed the documentation and tried running the comparison on the example files got this error: ``` (happy) meshari@MacBook-Pro-3 hap.py-master % sudo docker run -it -v pwd:/data 47b2428b563f /opt/hap.py/bin/hap.py...
Hi, I installed hap.py with apptainer. When trying to run with the following command: apptainer run hap.py_latest.sif /opt/hap.py/bin/hap.py truth.vcf comp.vcf -f HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed -o HG002_hg38_comp -r full_path_to.fasta I get the following...
