plink2 score polygenic score

Minta Thomas

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Mar 25, 2019, 12:49:12 PM3/25/19

to plink2-users

Hi Christopher,

In plink2,while generating polygenic risks core using --score option on vcf files, would it work directly on dosage data or hard calls?

If I want to use only dosage, not hard calls which are the prameters I need to include with --score.

Regards,

Minta

Christopher Chang

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Mar 25, 2019, 12:57:16 PM3/25/19

to plink2-users

The plink 2.0 --score implementation handles hard-calls and dosages in the same manner.

Minta Thomas

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Mar 25, 2019, 1:02:56 PM3/25/19

to Christopher Chang, plink2-users

Thanks for quick reply.

Could you please share the plink command to calculate polygenic risks score using dosage data directly from the vcf files?

Regards,

Minta

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

Christopher Chang

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Mar 25, 2019, 3:13:19 PM3/25/19

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Assuming the VCF dosage data is represented in "DS" form:

plink2 --vcf <name of VCF> dosage=DS --out converted

plink2 --pfile converted --score <name of score file> [other scoring options]

Replace "dosage=DS" with "dosage=GP" if only 0..1-scaled genotype probabilities are stored in the VCF.

On Monday, March 25, 2019 at 10:02:56 AM UTC-7, Minta Thomas wrote:

Thanks for quick reply.
Could you please share the plink command to calculate polygenic risks score using dosage data directly from the vcf files?
Regards,
Minta

On Mon, Mar 25, 2019 at 9:57 AM Christopher Chang wrote:

The plink 2.0 --score implementation handles hard-calls and dosages in the same manner.

On Monday, March 25, 2019 at 9:49:12 AM UTC-7, Minta Thomas wrote:
Hi Christopher,
In plink2,while generating polygenic risks core using --score option on vcf files, would it work directly on dosage data or hard calls?
If I want to use only dosage, not hard calls which are the prameters I need to include with --score.
Regards,
Minta

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Minta Thomas

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Mar 25, 2019, 5:34:19 PM3/25/19

to Christopher Chang, plink2-users

Thanks a lot for the quick reply and help!

On Mon, Mar 25, 2019 at 12:13 PM Christopher Chang <chrch...@gmail.com> wrote:

Assuming the VCF dosage data is represented in "DS" form:

plink2 --vcf <name of VCF> dosage=DS --out converted
plink2 --pfile converted --score <name of score file> [other scoring options]

Replace "dosage=DS" with "dosage=GP" if only 0..1-scaled genotype probabilities are stored in the VCF.

On Monday, March 25, 2019 at 10:02:56 AM UTC-7, Minta Thomas wrote:

Thanks for quick reply.
Could you please share the plink command to calculate polygenic risks score using dosage data directly from the vcf files?
Regards,
Minta

On Mon, Mar 25, 2019 at 9:57 AM Christopher Chang wrote:

The plink 2.0 --score implementation handles hard-calls and dosages in the same manner.

On Monday, March 25, 2019 at 9:49:12 AM UTC-7, Minta Thomas wrote:
Hi Christopher,
In plink2,while generating polygenic risks core using --score option on vcf files, would it work directly on dosage data or hard calls?
If I want to use only dosage, not hard calls which are the prameters I need to include with --score.
Regards,
Minta

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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Minta Thomas

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Mar 25, 2019, 7:49:36 PM3/25/19

to Christopher Chang, plink2-users

Hi,

Then what is difference between

plink2 --vcf <name of VCF> dosage=DS --out converted

plink2 --pfile converted --score <name of score file> [other scoring options]

and

plink2 --vcf <name of VCF> dosage=DS --score <name of score file> [other scoring options]

Christopher Chang

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Mar 25, 2019, 8:08:24 PM3/25/19

to plink2-users

The difference is that, in the second case, plink2 converts the entire VCF and then throws away the result. This is inefficient unless you never intend to use plink2 on the VCF again.

On Monday, March 25, 2019 at 4:49:36 PM UTC-7, Minta Thomas wrote:

Hi,
Then what is difference between
plink2 --vcf <name of VCF> dosage=DS --out converted
plink2 --pfile converted --score <name of score file> [other scoring options]
and
plink2 --vcf <name of VCF> dosage=DS --score <name of score file> [other scoring options]

On Mon, Mar 25, 2019 at 2:34 PM Minta Thomas wrote:

Thanks a lot for the quick reply and help!

On Mon, Mar 25, 2019 at 12:13 PM Christopher Chang wrote:

Assuming the VCF dosage data is represented in "DS" form:

plink2 --vcf <name of VCF> dosage=DS --out converted
plink2 --pfile converted --score <name of score file> [other scoring options]

Replace "dosage=DS" with "dosage=GP" if only 0..1-scaled genotype probabilities are stored in the VCF.

On Monday, March 25, 2019 at 10:02:56 AM UTC-7, Minta Thomas wrote:

Thanks for quick reply.
Could you please share the plink command to calculate polygenic risks score using dosage data directly from the vcf files?
Regards,
Minta

On Mon, Mar 25, 2019 at 9:57 AM Christopher Chang wrote:

The plink 2.0 --score implementation handles hard-calls and dosages in the same manner.

On Monday, March 25, 2019 at 9:49:12 AM UTC-7, Minta Thomas wrote:
Hi Christopher,
In plink2,while generating polygenic risks core using --score option on vcf files, would it work directly on dosage data or hard calls?
If I want to use only dosage, not hard calls which are the prameters I need to include with --score.
Regards,
Minta

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

Minta Thomas

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Mar 25, 2019, 8:18:03 PM3/25/19

to Christopher Chang, plink2-users

In plink2, will the --vcf option use the default hard call threshold 0.1, in this case?

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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Christopher Chang

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Mar 25, 2019, 8:19:49 PM3/25/19

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Yes, but that won't matter for --score since it uses dosages when available.

On Monday, March 25, 2019 at 5:18:03 PM UTC-7, Minta Thomas wrote:

In plink2, will the --vcf option use the default hard call threshold 0.1, in this case?

To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users+unsubscribe@googlegroups.com.

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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with regards,
Minta Thomas

"There is no peace more wonderful than the peace we enjoy when faith shows us God in all created things.”

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