Hi guys, I wonder if you guys can offer any advice!!
I am currently trying to call all SNPs from a set of 8 genomes in .bam file format from a single population. The genomes have been mapped and aligned, however I have no reference so cannot make an index from this.
I am using samtools, and have tried to create and index, resulting in .bai files from the bam files themselves. I have tried mpileup with with all 8 files but has taken over 2 hours so far to process. I did run the same for 1 of the files (took around 1 hour), which gave an incomprehensible .bcf file. Is it normal to take this amount of time? I am more than open to trying other tools should you recommend them. Thanks in advance for you help!