I am completely new to this field so I'm hoping this is a simple mistake on my part.
I'm trying to find the number of SNPs, indels and MNPs in a merged data set I have on Galaxy. This merged data set consists of 3 pairs of paired ended data and before merging, I have preprocessed the data (FastQC Read, FASTQ Groomer), mapped the data with BWA for Illumina, filtered my SAM files and specified read groups before variant calling.
When I try to run the Freebayes tool on the merged data set, I encounter the following error message: Fatal error: Exit code 1 () unable to find FASTA index entry for ''
I searched this forum for a similar request and I believe I am using the right reference genome (hg19) and have consistently used this genome throughout my analysis: Need help with "VCFgenotype-to-haplotype:" tool
Any assistance for this issue is appreciated!