How to know the shared mutations in test_ctDNA()

[esraa-jamal]

Hi,
Thank you for this tools ... I have a question please , Is there a way to know the mutations shared in between the tumour and ctDNA in positive samples ??

Thank you in advance,
Best,
Esraa

[alkodsi]

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 individual mutations. If you are interested in quantifying the ref and alt reads supporting your individual mutations, you can use this function: https://alkodsi.github.io/ctDNAtools/reference/get_mutations_read_counts.html

[esraa-jamal]

Thank you very much for your reply, I tried both functions (get_mutations_read_count and get_mutations_read_names) but the output was a little bit confusing for me... Could please explain to me how to read the output of both functions or what I am expecting to see??
because I thought that by using (get_mutations_read_names) function, it will give me the mutation names but instead it gave the BAM file name with numbers next to it .. are these numbers the positions of the mutations or what??

sorry to be a pain,
best,
Esraa

[alkodsi]

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 returns the number of reads supporting the reference and alternative alleles