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DReichLab / AdmixTools

Tools test whether admixture occurred and more
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Do any of the tools require genetic map distances for accuracy #73

Closed geneanalyst closed 3 years ago

geneanalyst commented 3 years ago

When Plink data is converted to Eigenstrat the genetic map distances are not added to column 3 of the .snp file. In other words column 3 of the .snp file has zeros.

Do any of the codes within Admixtools (F2s, qpAdm, qpdstat, etc ) rely on genetic map distances for accuracy ?

If so I can add them to column 3 of .snp from my Hapmap B37 recombination rate reference

bumblenick commented 3 years ago

You should use genetic map if possible; ROLLOFF and DATES which are strictly outside ADMIXTOOLS really require it.

I will look into the map conversion from PLINK.

Nick

On Fri, Mar 5, 2021 at 8:49 PM geneanalyst notifications@github.com wrote:

When Plink data is converted to Eigenstrat the genetic map distances are not added to column 3 of the .snp file. In other words column 3 of the .snp file has zeros.

Do any of the codes within Admixtools (F2s, qpAdm, qpdstat, etc ) rely on genetic map distances for accuracy ?

If so I can add them to column 3 of .snp from my Hapmap B37 recombination rate reference

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geneanalyst commented 3 years ago

Are F2s or F3s or qpAdm affected if genetic map is missing from .snp ?

FYI, Plink messes the order of the reference and alternate allele. I've noticed that within .snp column 5 is for REF and column 6 for ALT. However conversions from Plink map often result in REF being placed in col 6 of .snp and ALT in col 5.

Although I'm not sure whether that affects MAF calculations within Admixtools, I have taken the precaution of correcting the misplaced placement of REF into column 6 of .snp using my Hg19 reference genome.

Additionally, I commonly see "X" placed into column 6 of .snp (ALT column) in conversions from Plink map. I have no idea what "X" stands for

bumblenick commented 3 years ago

1) f-stats are not affected by the map but std, errors and Z scores are 2) X means that the alternate allele is unknown.

N

On Fri, Mar 5, 2021 at 9:40 PM geneanalyst notifications@github.com wrote:

Are F2s or F3s or qpAdm affected if genetic map is missing from .snp ?

FYI, Plink messes the order of the reference and alternate allele. I've noticed that within .snp column 5 is for REF and column 6 for ALT. However conversions from Plink map often result in REF being placed in col 6 of .snp and ALT in col 5.

Although I'm not sure whether that affects MAF calculations within Admixtools, I have taken the precaution of correcting the misplaced placement of REF into column 6 of .snp using my Hg19 reference genome.

Additionally, I commonly see "X" placed into column 6 of .snp (ALT column) in conversions from Plink map. I have no idea what "X" stands for

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/DReichLab/AdmixTools/issues/73#issuecomment-791846266, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEE77B4LGKJ6TYQR4VMMBTDTCGIYPANCNFSM4YWGC2IQ .

geneanalyst commented 3 years ago

Thanks!

2- I've been replacing "X' with ALT from my Hg19 reference genome.