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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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Super cool tool! Maybe in the README mention that FASTQ files are required if using the container #15

Closed jelber2 closed 2 years ago

jelber2 commented 2 years ago

As far as know, inputting FASTA reads aligned to the reference as the bam file will result in Pepper failing to find any variants using the default settings of the Docker/Singularity container as the config for Pepper requires a minimum base quality setting.

mikolmogorov commented 2 years ago

Hi,

I think it should work with fasta in theory. Could you give a specific error output that you are getting?

jelber2 commented 2 years ago

Hmmm. I was getting issues with PEPPER generating empty VCF files for input to margin. I simply ran Singularity. Deleted the pepper directory, restarted, and now it is working as far as I know?

jelber2 commented 2 years ago

I will close this.