hap.py
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Illumina
Haplotype VCF comparison tools
I use command python /opt/hap.py/bin/hap.py trust.vcf test.vcf.gz -T /data/target.bed -o ./test In summary file，filter column，I can see ALL,PASS，But i didn't find the location filtered, how to find it?thks
I have performed validation of the tools using python 2.7.18 with all of the required packages and am happy with how it all works. With the python 2.x sunsetting having...
I can't get the versions of `pre.py` and `hap.py`: ``` $ hap.py --version Hap.py ``` and ``` $ pre.py --version usage: VCF preprocessor [-h] [--location LOCATIONS] [--pass-only] [--filters-only FILTERS_ONLY] [-R...
When installing `hap.py` via Conda, `rtg-tools` is not a dependency for the `hap.py` package and requires additional installation steps. While the manual install/build notes mention using the `--with-rtg-tools` flag, this...
I am currently doing benchmarking of the VCF files with the gold standard file **HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_PGandRTGphasetransfer.vcf**. While I am giving both the query as well as the truth as the GIAB...
i have installed pandas, still i am getting this traceback Traceback (most recent call last): File "bin/hap.py", line 41, in import Tools File "/home/monika_mohite/hap.py-build/lib/python27/Tools/__init__.py", line 102, in import pandas #...
`# hap.py NA12878.vcf.gz 01.Raw_variants.vcf.gz -f ConfidentRegions.bed.gz -o test -r hg38.fa ` ``` [I] Total VCF records: 4167900 [I] Non-reference VCF records: 4167900 [W] overlapping records at chr1:37070742 for sample 0...
Hi i seemed to have problem running the octopus vcfs file by either using legacy/ non-legacy file I tried using --no-leftshift --no-decompose --gender=none but it does not work cts/2019_MLVarCaller/01_BAMs/hs37d5.fa -f...
Hi, I install the hap.py through anaconda. When I run the test run: $ hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -r example/chr21.fa -f example/happy/PG_Conf_chr21.bed.gz -o test I get something error. May someone help...
