The parameter setting about neat-genreads HOT 3 CLOSED

Greetings!

Thanks for catching the typo in the readme, both of them should've been the same number (in this case, 101). Additionally, I added a description of the WP field to the output VCF header.

The WP flag is used internally by genReads to determine which set of chromosomes to insert mutations on (WP stands for "which ploid"). Basically it gives you phasing information, for human (diploid) the possible values are WP=0 (occurs on first chromosome, so a heterozygous variant), WP=1 (occurs on the other chromosome, also heterozygous) or WP=0,1 (occurs on both chromosomes, so homozygous).

Hope this helps!

from neat-genreads.

Thanks, Zack!
So 0 or 1 just stands for the occurring site of which chromosome instead of the variants occurring or not (0= none, 1 = variant)?
I'm confused by these two for explaining them.
WP = 1/0
WP = 0/1
Are there any differences?

from neat-genreads.

The index of the zeros and ones indicate which chromosome copy the mutation is present on. Basically it provides phasing information. For example, if we were simulating triploid data:

WP=1/0/0 would indicate a mutation on the first chromosome copy only (so expected allele fraction in the alignment would be ~33%)
WP=0/0/1 would indicate a mutation on the third chromosome copy only
WP=1/1/0 first and second copy (so expected allele fraction ~66%)
WP=1/1/1 present in every chromosome copy (AF=100%)

Hope this helps!

from neat-genreads.