hap.py
hap.py copied to clipboard
Illumina
Haplotype VCF comparison tools
Hello, I’ve been using hap.py to benchmark two VCF files, but I keep encountering the following warning: [W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Number=0 I’ve tried modifying...
Hi, thanks for the great tool! I’ve stumbled on a bug that causes FP variant calls when performing a pairwise comparison of VCFs (xcmp mode) while when taking all variants...
The current docker image is 7 years old and is not supported in many systems. Can a new docker image with latest code change created?
I use docker to start hap.py. The docker sentences: ``` docker run -it \ -v "${PWD}":"/input" \ -v "${PWD}/my_output:/output" \ jmcdani20/hap.py:v0.3.12 /opt/hap.py/bin/hap.py \ /input/chr20.vcf.gz \ /output/my.vcf \ -f "/input/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_chr.bed" \...
For the NA12878 sample, I used a high-confidence BED file (e.g., GIAB high-confidence regions) and intersected it with the capture targets from whole exome sequencing. Within this intersected BED region,...
Hello, I am experimenting happy running with rtg vcfeval engine, and a potential bug (or an error from my side) took my attention. Running happy with rtg vcfeval engine didnt...
Hi, First of all, thanks a lot for your great work on this project! Since the project has been archived and the official Docker image is outdated, it's a bit...
I am grateful for the tool. I run the ONT data with Tumor only with pepper-DeepVariant, so I don't have the Normal-matched tumor to call the truth-vcf file. Can I...
Hello, Hope you can help me! I called variants with deepvariant v1.8.0 for my region of interest, and then I wanted to bnchmark them with hap.py ``` # Define the...
We are using hap.py to compare various sequencing runs processed via the DRAGEN pipeline. In the DRAGEN output vcf, any variant with a VAF of at least 0.01 is reported....
