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odelaneau / shapeit5

Segmented HAPlotype Estimation and Imputation Tool
https://odelaneau.github.io/shapeit5/
MIT License
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ERROR: Opening [info/target.haploid.txt]: file format not supported by HTSlib #42

Closed Ilaria-Pirona closed 1 year ago

Ilaria-Pirona commented 1 year ago

Good morning, I am trying to use your program using the data in the test folder. Following the commands present in phasing chromosome X data (link) and using the container quay.io/biocontainers/shapeit5:1.0.0--h0c8ee15_0 I get the following error:

SHAPEIT5_phase_common --input array/target.haploid.bcf --reference info/target.haploid.txt --region 1 --map info/chr1.gmap.gz --output target.phased.bcf --thread 8

ERROR: Opening [info/target.haploid.txt]: file format not supported by HTSlib

Can you help me figuring out which is the problem? Thank you

theandyb commented 1 year ago

It looks like you're passing the list of haploids to the --reference option and not the --haploids option as it is written in the tutorial. The error is in response to the program expecting a VCF/BCF file to be passed as the reference option (as is done in the 4th usage example).