Amjad Alkodsi

The problem is when paired end reads are overlapping, such as the example below: ``` Read1 (first pair): ------------------ACGT Read1 (second pair): ACGT-------------------- ``` the pileup function will count the...

Hi Alexis, The test_ctDNA function will look at the mutations collectively and see if the support is exceeding what can be expected by chance. It doesn't call positive or negative...

Hi Esraa, The test_ctDNA function will look at the mutations collectively and see if the support is exceeding what can be expected by chance. It doesn't call positive or negative...

Hi Esraa, get_mutations_read_names will give you the bam read IDs for the reads that support reference and alternative alleles. get_mutations_read_count is the function that you would need to use. It...

Hi @rpauly The normalized counts are expected to be NaN if the not normalized counts are all 0. As to why the counts are 0, I can't tell without debugging...