I'm analyzing the exome sequencing data and plan to retrieve the nucleotide counts of specific positions from Bam files. I am a beginner of bioinformatics. My friends said pysamstats is a good software. If you have a information, would you please tell me what software is best and how can I do that?
I wanna get the nucleotide frequency of 5000 SNPs.
chr1 2000454 A:5 T:546 C: 2
chr2 230404 A:1 T:2 C:343
chrx 3234343 A:323 T:1