Should we/when should we exclude chrM/X/Y in our analysis? #165
hsun3163
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Default analysis setting
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No we only consider chroms 1-22. |
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you might want to add an interface somewhere to remove other chroms... ? |
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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.
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