telomerecat

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Hello, first of all thank you for developing such an important tool. I have recently tested telomerecat with a lot of WGS at 30x coverage and the results seemed a...

victortoledo

Zero length estimates

4

Hi, For some samples I get an estimated length of 0. What they all have in common is that F2a is negative (i.e. F4 > F2, because F2a = F2...

kgori

Parabam undefined variable?

1

Today I found another small defect while running another sample through, this time in parabam, probably that code path is not being hit that often?: ``` Traceback (most recent call...

brainstorm

Hi, As of Jan 2020 python 2 is unsupported and there is no guarantee that you will be able to install dependencies after this date. Are there any plans to...

keiranmraine

Hi, It would be useful if the documentation and the readme would state that this software is python2, at least I could not find it and did create a python3...

messersc

De novo telomeres

1

How would telomerecat handle cases where a broken chromosome is stabilised by the _de novo_ gain of telomeres? Reads from newly formed 'sub-telomeric' regions ought to map within the original...

Adamtaranto

https://github.com/jhrf/telomerecat/blob/af558f51bbe21a55c23b0fafe8961e47c67bebd8/telomerecat/telbam2length.py#L457 File "/usr/local/lib/python2.7/site-packages/telomerecat/telbam2length.py", line 460, in __get_mean_and_sd__ x_sd = np.sqrt((x_N * x_power_2) - x_sum**2) / x_N AttributeError: 'long' object has no attribute 'sqrt'

chunyangbao

Backtrace on a COLO829 sample

2

Hello @jhrf, thanks for this piece of software! I have been running it for a few samples now, but there's one (non-empty, 22KiB BAM file with only telomeric regions from...

brainstorm