Hi,
Thanks for continuous efforts on updating Sentieon. I noted the example pipeline is kind of different from what I saw in the last year. If I remember correctly, previously, it is recommended to (1) realign the reads around indels (2) co-realignment of tumor and normal, and then run TNscope/TNhaplotyper/TNsnv. But now I see these steps are removed. My questions are:
Should I follow the up-to-date example script without indel realignment?
TNscope/TNhaplotyper/TNhaplotyper2/TNsnv, which one, from your experience, has the best performance and is recommended for mutation detection?
I see in the new example scripts, there are some filtering on mutations using BCFtools. Do I need to modify the parameters to make them suitable for different sequencing depth (My data is 30X WGS, tumor-normal paired)
Hi, Thanks for continuous efforts on updating Sentieon. I noted the example pipeline is kind of different from what I saw in the last year. If I remember correctly, previously, it is recommended to (1) realign the reads around indels (2) co-realignment of tumor and normal, and then run TNscope/TNhaplotyper/TNsnv. But now I see these steps are removed. My questions are:
Thanks in advance!
Best Yang