I am trying to run a workflow from a complete genome .bam file all the way to the consensus of a fasta sequence from the .vcf file constructed through the process.
After sorting, indexing, and retreiving a .bam file with the genic strand i wish to work with, i need to run
As i run the following command:
samtools mpileup -g -f MyFile.bam > MyFile.bcf
I get the following error:
[group_smpl] Read group SRC-5-alex4__MA167snp used in file MyFile.bam but absent from the header or an alignment missing read group.
Anyone who could help me figure out how to output a .bcf file successfuly?, I have run this command on docens of other genomes, and it's the first time i get an error. Any help would be much appreciated.