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Bug for nonPAR chrX: heterozygous haploids in the phased output.

2

Hi, When phasing non-PAR X, if present in the input VCF/BCF, the heterozygous haploids are not correctly set to missing. Here is the problematic code: ``` for (uint32_t v =...

dtaliun

Hi, Phasing results for chromosome X non-PAR regions are wrong when providing input VCF/BCF files with haploid male genotypes represented as 0 and 1 instead of 0/0 and 1/1. The...

dtaliun

Segmentationfault (core dumped) in one Chromosome

2

I have been getting a segmentation fault when running phase_common_static. I am using the latest version, and frankly, it's been working perfectly for me as I have used it a...

NattyandMinnie

I have an unusual observation regarding the AN field in the output file of phase_common. It appears that the AN field in the output file is calculated as the sum...

lessdata

phase_common failing at PBWT step

2

I'm using SHAPEIT5 to phase a large panel (300K+) using phase_common and it keeps stopping at the PBWT step? This is the relevant error: > WARNING: No PBWT states found...

nmshahir

file extention not recognized

8

Hi, I am trying to use shapeit5 for the first time. I tested the "test" script and it works. I am getting this error for the output file `ESC[31mERROR: ESC[0mFilename...

marlmatos

Port shapeit5 to MacOS on Apple Silicon using SIMDE

11

There's demand for users to be able to run shapeit on Mac OS, with users who want that creating Github issues or asking on other discussion forums: https://github.com/odelaneau/shapeit4/issues/15 https://github.com/odelaneau/shapeit4/issues/36 https://github.com/odelaneau/shapeit5/issues/22...

pettyalex

illegal instruction error on phase_common_static on cow array data

2

Hi I'm trying to run phase_common_static on my cow array data, and blocked with this error: phase_common_static --region 1 -I huellas.vcf.gz -O huellas_prueba.bcf --log log.txt -T 8 [SHAPEIT5] phase_common (jointly...

lholivera

feature request: Mac OS and Linux ARM64 compatibility?

2

I've had multiple researchers on my team lose some time this week assuming that shapeit5 is Mac OS compatible, but it is not. At the same time, the major cloud...

pettyalex

Docker image - Static binaries shouldn't need host libraries

3

I noticed that the Docker image seems to include the libraries necessary to compile shapeit5, but does not compile them inside the docker container. Instead, static binaries from outside the...

pettyalex