Should we/when should we exclude chrM/X/Y in our analysis? #165
hsun3163
started this conversation in
Default analysis setting
Replies: 1 comment 1 reply
-
No we only consider chroms 1-22. |
Beta Was this translation helpful? Give feedback.
1 reply
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
In lots of times the analysis only take autosomal chromosome e.g. GRM module. But also in a lot of time the imput data may contains sex chromosome as well. So in our pipeline, when is a good time to exclude the sex chromosome?
A safe time to exclude them I think is when we partitioned the whole genome plink into plink per chrom.
p.s. As GRM for chrM/X/Y , APEX association scan can not be done on these chromosome.
Beta Was this translation helpful? Give feedback.
All reactions