I am performing Variant calling using the following protocol https://galaxyproject.org/tutorials/var_hap/
I want to compare 2 experimental samples (paired-end reads) against the reference Pseudomonas aeruginosa PAO1 genome. I mapped both these experimental samples against PAO1 (I input the fasta sequence from NCBI and used bwa to index, then mapped using bwa-mem. I merged the 2 sets of bam files, removed duplicates which produced one bam output file. I input this bam file into the BamLeftAlign tool, used the default pseudomonas aeruginosa PAO1 reference genome from the drop-down arrow, with max 5 iterations. I received the error: unable to find FASTA index.
Could not display BAM file, error was:
file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False
In the protocol, they use the same bam output file after removing duplicates, so I am unsure what is wrong here?