Inconsistent SNP Numbers in DART Package

[NURUL AFIA ABD. MAJID]

Hello admin,

I am attempting to filter the SNP dataset using certain parameters in the dart package. However, when I run the same parameters for the second time using the same dataset, it appears to have different SNP numbers. Is this a usual occurrence, or is there a problem in my filtering process?

[Arthur Georges]

Hi Nurul,

Some of the filters have a random element to them. For example, gl.filter.secondaries will filter out all but one SNP on sequence tags with multiple SNPs, and it picks the one to retain at random (by default).

This will affect the outcome of subsequent filtering, and so the number of retained SNPs will vary from run to run (albeit only slightly).

I expect that is the reason.

Arthur

On Mon, 6 May 2024 at 02:58, NURUL AFIA ABD. MAJID <afiam...@gmail.com> wrote:

Hello admin,

I am attempting to filter the SNP dataset using certain parameters in the dart package. However, when I run the same parameters for the second time using the same dataset, it appears to have different SNP numbers. Is this a usual occurrence, or is there a problem in my filtering process?

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[NURUL AFIA ABD. MAJID]

thank you 

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