hap.py

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Another Hap.py installation error related to stdc++

1

I am trying to install Hap.py on an HPC Cluster that I do not have administrative access to. After running cmake and make, I get the following errors: [ 50%]...

peterlchang

I run hap.py twice on the same vcf file - first time without an additional stratification file, and the second time with stratification for GC and Low complexity regions. I...

ofonov

Dear Hap.py authors, First, thanks a lot for Hap.py, it is an excellent tool. I've a question on the possibility of using Hap.py in order to assess the accuracy of...

elowy01

scmp-distance engine

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I am trying the local counting based on distance match using the scmp-distance engine but getting following error USAGE ``` /opt/hap.py/bin/hap.py tmp/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf.vcf.gz tmp/S1.genome.vcf.gz -R tmp/target_regions_merge.bed -o tmp/hap_test5 -r tmp/hg19.fa --engine...

virenar

Hi, I have used hap.py to measure performance and get a strange result in which at the highest value of my QQ field (QUAL = 228), a very low recall...

ksw9

hap.py annotated VCF file as output issues running with docker

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I am not running multisample VCF file anusha@Precision-7920-Tower:~/TESTBEN1$ sudo docker run -it -v `pwd`:/data pkrusche/hap.py /opt/hap.py/bin/hap.py /data/NA12878.vcf.gz /data/PRO001B.vcf.gz -r /data/genome.fa -f /data/ConfidentRegions.bed.gz -V -o PRO001B_happy --no-leftshift --no-decompose --gender=none --engine=vcfeval [sudo]...

achimmiri

Docker

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Hi Peter i have couple of questions, please 1. i try to define the reference location in both providing the -r parameter and exporting the HGREF variable the result is...

ktadler

Parsimony

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Dear all, I just only want to know, if pre.py realize the parsimony step for normalize... If is yes, i just only want to know which flag is related to...

Jordi-V

ERROR [stderr] regex_error

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Dear, when i run this hap.py Standard.wes.vcf Standard.wes.vcf -o NA12878 --threads 6 it produced 2018-11-03 14:53:14,187 ERROR [stderr] regex_error 2018-11-03 14:53:14,199 ERROR Command 'quantify /tmp/hap.py.result.P5wuqJ.vcf.gz -o NA12878.roc.tsv -r /data/Reference/fasta/hs.grch38.fa --threads...

Xingsl

Is it possible to output 0/0 and ./. positions in VCF?

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Hi, the thing is that when I input a VCF file with positions with ./. and 0/0 pre.py removes them from the final vcf file, I understand that there are...

afzm