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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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read depth calculation #80

Open abrozzi opened 7 years ago

abrozzi commented 7 years ago

Hi, how each allele read depth is calculated? The read depth that I find in the output (column "depth") is the average of each one of the seven loci read depth? And for each locus the read depth is in turn an average of all depths of the alleles?

Thank you in advance

abrozzi commented 7 years ago

Hi,

in the body of function read_pileup_data (LINE 314 of srst2.py) the following lines:

allele_line = 1 # Keep track of line for this allele allele_line += 1 avg_depth = round(total_depth / float(allele_line),3)

makes the length of each allele longer of 1 base.

HTH

katholt commented 7 years ago

The reported read depths represent the top scoring alleles only (one per locus).