zhixingfeng/iGDA

haplotype frequency

antoine4ucsd opened this issue · 4 comments

antoine4ucsd commented

Hello
is there an option to store frequency, Avg Coverage, num reads, for each haplotype ... that would be nice to save it in the fasta header for each. thank you and congrats for all the good work!

zhixingfeng commented

Hi antoine4ucsd,
Frequency is not wrapped into fasta files in the current pipeline, but reads count for each contig can be found in the .count files in the intermediate results.

Or, there is an internal CLI "igda abundance" can yield reads count for each contig. You might have a try on that using the intermediate results as input.

Best

Zhixing

antoine4ucsd commented

thank you . reads.count is already a good metric to get. Frequencies and counts in contig names would be something nice to add in the future.

antoine4ucsd commented

Hello
I am analyzing a new set of NP data. I have interesting results but I would like to have the abundance (and ideally the mean coverage) for each haplotype. is it something I can get from igda?
all suggestions are welcome

thank you@

PeienJ commented

Hello Zhixing,
Could you please give an example of how to use "igda abundance" or .count files? There are many intermediate files and I started to be confused about which file I should use. Thanks!!