hap.py
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Illumina
Haplotype VCF comparison tools
Blocksplit consistently failing with: W] overlapping records at chr1:3181487 for sample 0 [W] Variants that overlap on the reference allele: 664 [I] Total VCF records: 5088629 [I] Non-reference VCF records:...
I can't get rid of this: ``` root@86876e01e030:/outputs# /opt/hap.py/bin/hap.py --threads $(nproc) --gender auto --reference /outputs/ref/human_g1k_v37/human_g1k_v37.fasta --false-positives /outputs/precFDA/challenge4-fullset.bed --report-prefix /outputs/test012_07_NovoalignGATKHC_1_src /outputs/precFDA/challenge4-fullset.vcf.gz /outputs/precFDA/challenge_results/NovoalignGATKHC_1.vcf.gz 2019-09-10 15:26:22,969 WARNING No reference file found at default...
Hi, I have validated my detect result use hap.py/som.py and just compare [chorm-pos-alt-ref]，but these two functions showed different results. for example, I have test strelka2 with dataset NA12878, the som.py...
I was trying to run hap.py with --preserve-info using vcfeval as a comparison engine, but it keeps on throwing an error about an undefined variable `output_vcf`. The offending line is...
When GATK tools HaplotypeCaller + GenotypeGVCFs report multiple alleles, one of which is a deletion, the AD field may contain an "extra" entry. This causes hap.py to emit a warning,...
when try to install hap.py through: `python install.py ~/hap.py-install --with-rtgtools` I got an errror with this step: `cd /home/enrico/hap.py-install && /home/enrico/app/benchmarking-tools/tools/hap.py/src/sh/run_tests.sh` > 2020-09-04 13:10:45,567 WARNING No reference file found at...
We want to look at concordance for specific chromosomes. If we can extract the variants from the vcf file that hap.py outputs (the file with all the tags like FP,FN,TP...
HI First of all, thank you for the program that is useful for comparing. I'm a little confused, but when I draw a PR curve, I use the QQ value...
Hello, I noticed pre.py errors out on the HLA contigs when I use a VCF called against all contigs in the hg38 assembly. I have been able to successfully run...
Upon running "python install.py ~/hap.py-install", I get the following error message: -- Configuring incomplete, errors occurred! See also "/tmp/buildMYGaCE/CMakeFiles/CMakeOutput.log". cd /tmp/buildMYGaCE && make -j16 make: *** No targets specified and...
