I have programmed a simulator which creates SNPs at random locations in the genome (using a fasta). My program generates an output fasta file with the SNPs in place. I wanted to test it out so I made my reads using dwgsim keeping all errors at zero (such that it only creates reads).
I then used novoalign to get my sam file. (aligned the reference file and the reads generated by dwgsim)
Then using samtools tools I converted the sam file to bam and sorted the bam file.
Now when pileup, the outfile is empty.
Is there a specific condition samtools uses to call SNPs?
I then used novoalign to get my sam file. (aligned the reference file and the reads generated by dwgsim)
Then using samtools tools I converted the sam file to bam and sorted the bam file.
Now when pileup, the outfile is empty.
Is there a specific condition samtools uses to call SNPs?
