I have deep sequencing of an amplicon (~1,000,000x), and would like to count the number of reads that show an A,C,G or T at a particular position of a BAM file. I'm not concerned with indels currently. I have previously used the fifth column of
samtools mpileup, but due to the high depth, this format is not ideal. Which other tools can you suggest? Is there a standard way to store this read-support information in a VCF file?