Can PLINK2 allow for the direct input of the RFMix output (the MSP file) ?

[Charlie Sun]

Hello,

Does anyone know how to use the RFMIX output as direct input for plink2 to run on association analysis with local-covar   ?   I tried but it gave me the error.

Thanks,

Charlie

-bash-4.2$ plink2  --threads 20 --pfile AAGWAS_chr22 --glm local-covar=chr22.msp.tsv local-psam=AAGWAS_chr22.psam local-pos-cols=2,1,2,7  --ci 0.95  --out AAgwas_chr22_gloAFR_locAFR_test
PLINK v2.00a2.3 AVX2 (24 Jan 2020)             www.cog-genomics.org/plink/2.0/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to AAgwas_chr22_gloAFR_locAFR_test.log.
Options in effect:
  --ci 0.95
  --glm local-covar=chr22.msp.tsv local-psam=AAGWAS_chr22.psam local-pos-cols=2,1,2,7 local-haps
  --out AAgwas_chr22_gloAFR_locAFR_test
  --pfile AAGWAS_chr22
  --threads 20

Start time: Sun Jul 31 21:50:05 2022
Error: Invalid --glm parameter 'local-pos-cols=2,1,2,7'.
For more info, try "plink2 --help <flag name>" or "plink2 --help | more".

[Christopher Chang]

Please retry this with a more recent plink2 build.

[Charlie Sun]

Yes, it works with the most  recent plink2 build.

Thanks,

Charlie