haplotype frequency

[antoine4ucsd]

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]

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]

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]

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]

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!!