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On line 261:

base_qual = ord(read.alignment.qual[read.query_position])-33

read.query_position will be None if is_del or is_refskip are set.

http://pysam.readthedocs.org/en/latest/api.html#pysam.PileupRead.query_position

Create dictionary where keys are read names as an efficient way of checking if a read has already been processed

Hello,
When running augment_maf.py for trios(N/T1/T2) the t_depth data in the generated mafs would be the same as the first maf file in the command no matter what the bam files is (T1 or T2). So if we want to generate aug.maf for T2 and use the T1 maf first in the command, that will give us t_depth data of T1 instead of T2 . Apparently the script does not update the t_depth information in the maf file and just use the present data in the first maf file.

Thanks,
Arezoo

If we intend to continue using augment_maf to summarize/capture allele count information we should consider a way to allow it to be run in parallel. The problem is particularly worsened in FFPE genomes due to a much higher (raw) mutation load from tools such as Strelka. A simple extension would be to allow a genomic interval to be specified.

1. When calculating the genome-wide coverage, obtain number of mapped and non-duplicate reads (as opposed to just mapped).
2. When calculating the target coverage, exclude reads marked as duplicated