Would anyone please be able to help me with the following, I am new to sequencing analysis:
Input Data: .bam file with thousands of reads .fasta file with my reference
When I align my .bam file reads to my reference using IGV I get a coverage track displaying the depth of the reads at each locus as a grey bar, and coloured bars with the proportion of each base (A, C, G, T), insertions and deletions, at "low quality" read sites. These are the values I am interested in.
What I would like now, would be to export these values so I can work in Python. How may I achieve this?
Or is there a more direct way of calculating the same values directly in python with say pysam that I have not found yet?
In IGV you can export the counts using IGVtools to .tdf or even .wig, but I am restricted to IGV to read them afterwards, and would prefer a more direct method.