I am a newbie to GATK. I have started the best practices pipline but stuck in bwa. From where can I get the reference.fa file? The GATK bundle has .fasta .bam .fai but no .fa. Anyone please!
The .fasta file can be used as the .fa file.
Thank you very much @Sheila .. I tried it earlier but it result in an error. I will try again and come back in case !