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zhixingfeng / iGDA

Detect and phase minor SNVs from long-read sequencing data
GNU General Public License v2.0
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usability tweaks #7

Open aretchless opened 2 years ago

aretchless commented 2 years ago

Hello. Thank you for developing and sharing iGDA. While testing it out, I noticed a few features that could make it more useful to end-users, in case you decide to do additional development on iGDA.

  1. Report SNVs in a standard human-readable format (e.g. 484K). Right now, they are encoded "for each integer x, floor(x/4) = 0-based locus, and x modulo 4 = base (0=A, 1=C, 2=G, 3=T)"
  2. Report proportions, both for the individual SNV (detected_snv.vcf) and for the contigs if possible.
  3. As I understand the current report format, there is no indication whether or not the 'reference genotype' is present in the sample; genotypes are only reported if they have SNVs.

Thanks Adam

zhixingfeng commented 2 years ago

Hi Adam,

Thank you for your insightful comments on iGDA. We are actively working on a major update of iGDA to include several novel features, and will make the output more informative in the next release. Regarding the SNV frequency, a workaround at this point is to look at the intermediate results which contains the pileup of reads. Or use "igda pileup" to obtain the pileup, where "m5file" can be obtained by "igda samtom5".