T parameter help

[gianfilippo]

Hi,

I am trying to understand the how to properly choose fix the T parameter, which I understand is the min threshold for the O22 value (i.e. observed count of the 2-haplotype).

I am running one SARS-cov-2 sample (amplicon sequencing on Illumina) I am interested in. I ran it with Tf=0.05 and T=1,10,100. Summary results are below.

Could you please explain me how T is affecting number of SNVs and haplotypes ?

SNVs numbers: T=100 2412 T=10 3871 T=1 2491

Haplotypes N and freq: T100: 0_fr_0.2847895994964371, 1_fr_0.19215312905857715, 2_fr_0.19203620837052798, 3_fr_0.1624256254050896, 4_fr_0.06115178494543045, 5_fr_0.05772617687199445 T10: 0_fr_0.2676417679182119, 1_fr_0.26451591468463653, 2_fr_0.15307681215147081, 3_fr_0.08339144250951734, 4_fr_0.08243902008443806, 5_fr_0.08039214779779189, 6_fr_0.06854289485393335 T1: 0_fr_1.0

Thanks