I'm new to this business, so my question may seem as dumb. I want to make an mpileup file using a reference sequence and several (two to begin with) aligned sorted BAM files. And I want the output file to have certain easy-to-read tab-delimited formatting (which is helpful for subsequent analyses of the output file):
field 1 - chromosome,
field 2 - position,
field 3 - reference base,
field 4 - base(s) in SAMPLE1.BAM for position in field 2,
field 5 - number of reads supporting bases in field 4,
field 6 - base(s) in SAMPLE2.BAM for position in field 2,
field 7 - number of reads supporting bases in field 6.
Something like shown below:
field1 field2 field3 field4 field5 field6 field7 Chr1 15967 T T,A 15,17 T,_ 25,_
where _ means no alternative (or second) base (or zero reads) for this position in the BAM file. '0' or empty space (or nothing) instead of _ is ok. It's ok if information in fields 4-7 is shown not in a single field but in several fields.
Which command is suitable for such a purpose? Thank you.