hap.py

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PreProcessing creates un-ordered VCF

1

Error message: ``` Exception: Command line bcftools index -t /tmp/tmpIg13Dm.vcf.gz got return code 255.STDOUT: STDERR: [E::hts_idx_push] unsorted positions on sequence #5: 38598232 followed by 38598227index: failed to create index for...

MattWellie

output_vcf

1

Where this variable is defined "output_vcf" in hap.py script ??

Shreya-droid

Don't find the reference

1

**CODE:** hap.py 40X_deepvariant_illumina_tumor_only.vcf 40X_PEPPER_MARGIN_tumor_only.vcf -r /public/groups/vg/xkang12/data/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta -o hap_result/ **ISSUE:** WARNING No reference file found at default locations. You can set the environment variable 'HGREF' or 'HG19' to point to a...

kangxiongbin

no genotype or ts/tv stratification

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I'm using hap.py with the docker image, but I don't get genotype or ts/tv stratification in the extended.csv, just '*'. Neither with my files or the example data. Example data...

mikyatope

If the input .vcf file contains wrong multi-line description of a single variant (usually at repetitive sequence), the pre.py will generate the same correct variant description for all these lines....

YuanfengZhang

segmentation fault at gvcf2bed

7

Hello, I'm running the hap.py v0.3.12 docker using the Genome In A Bottle HG002 vs GRCh38 truth set using the files below and getting a segmentation fault error in the...

meredith705

problems about default and customized ref.fasta in variant normalisation process

1

`##Reference=hg19`comment of output.vcf.gz never changes. There are two specific problems: 1. [hap.py/src/python/Tools/__init__.py](https://github.com/Illumina/hap.py/blob/master/src/python/Tools/__init__.py#L132) Line 132 No matter what ref is used, b37, hg19, GRCh37d5 or GRCh38... the writeVCFHeader will always output...

YuanfengZhang

I'm getting an error while trying to run hap.py. This is using a script I've successfully run many times. This is the stderr log from the run. ${HAPPY} $GIABSNPS q0.recode.vcf...

colinhercus

Calculation of METRIC.Precision

1

Dear hap.py development team, Could you please tell me, how the calculation for METRIC.Precision is done for the hap.py statistics summary? According to the [docs](https://github.com/Illumina/hap.py/blob/master/doc/happy.md), the following formula is used:...

b-math

Ubuntu 20 compatible or Python 3 Version

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Greetings! It is mentioned in README.md that "hap.py" is known to build and run on the following linux distributions: `Ubuntu 12.04,14.04,16.04,18.04 CentOS 5,6,7` My OS is Ubuntu 20.04. Is it...

tahirasma