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[GATK-4.1.2.0] FastaAlternateReferenceMaker - error "the input sequence contains invalid base calls"

Hi,

I want to make a 'pseudogenome or alternate fasta' using a VCF file generated using GATk-HC followed by HardFiltering and annotation using SNPeff. I do not find any issues when I use the 'FastaAlternateReferenceMaker' with a small interval mentioned to test if the program is behaving the way it should be and it is. Now when I apply it to the whole genome, I get the "the input sequence contains invalid base calls" error. I see that the issue is with the 'Reference' fasta file, am I right? If yes, I am not exactly sure what the problem is. I tried it with intervals that has some 'N' as well, apart from 'ACGT' and it works fine as well in small intervals. Grape genome that I am using: http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/12X/assembly/goldenpath/unmasked/

Can you please help me in finding out how to solve this? Please find the attached file for complete error note.

Thank you.
Sumanth

Answers

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