hap.py
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Illumina
Haplotype VCF comparison tools
I use hap.py to compare germline variants with engine=vcfeval. I see some variants line with BD=N. what's the meaning of "BD=N"? it's seems that variants called in both TRUTH and...
I'm using an academic HPC so the use of docker is not allowed due to security concerns. I would like to know how I can run `hap.py` using `singularity`: I'm...
I made a copy of truth.vcf.gz. Then I compare truth.vcf and it's copy (compare two identical files) by hap.py, and hap.py reported about 733 FN, (1197+253) FP. so, the recall...
Dear developer, I compared trueset file NA12877.vcf.gz( including SNP and IDNEL variants) with query file(only SNP variants). For the INDEL in summary.csv, there are numbers on TRUTH.TP TRUTH.FN columns, while...
Sorry to bother you. I tried a lot to build hap.py, but still failed. Can you release a binaries version which can working on linux, update the version on docker...
Hi Peter, I am using hap.py to compare vcf files against the GIAB reference in two separate runs for freebayes (freebayes.vcf) and GATK4 HaplotypeCaller (gatk.vcf), respectively. Both vcf files were...
Hello When I run som.py with -R option, I get such an error as: ``` Error running BCFTOOLS; please check your file for compatibility issues issues using vcfcheck 2020-02-20 21:42:22,860...
hap.py crashes after 10 hours of computation, presumably because it tries to allocate too much memory in RAM: peak RAM usage at termination is 117 GB on a system with...
I am running the command using Nextflow: ``` /opt/hap.py/bin/hap.py \\ $truth $filtered \\ -f $cr_bed \\ -o happy_annotated \\ -r $reference \\ --engine=vcfeval \\ --engine-vcfeval-template $sdf \\ -V \\ --preserve-info...
Hi, I've exported the Docker pkrusche/hap.py to a singularity image to run Hap.py The Hap.py command that run in the singularity image is as follows: `/opt/hap.py/bin/hap.py ${TRUTH} ${QUERY} -f ${BED}...
