Merge 4 CoreExome chip arrays files keeping only the overlapping/common variants
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Entering edit mode
21 months ago
fondan • 0

Dear members,

I have 250 samples which I want to do Quality Control and Imputation. These are distributed in 4 different datasets and 3 different array types.

(1) HumanCoreExome-12v1-1_A. 12 samples (2) InfiniumCoreExome-24v1-1_A 34 + 88 samples (3) InfiniumCoreExome-24v1-3_A1. 116 samples

gencall.smajor18.bed #143648 / gencall.smajor18.bim #551004 variants / gencall.smajor18.fam #116 people

gencall.smajor14.bed #14492 / gencall.smajor14.bim #542585 variants / gencall.smajor14.fam #12 people

gencall.smajor16.bed #81892 / gencall.smajor.16.bim #551839 variants / gencall.smajor.16.fam #34 people

gencall.smajor17.bed #109727 / gencall.smajor17.bim #551839 variants / gencall.smajor17.fam #88people

To my understanding, I should keep only the common variants across the 3 different types of arrays. What is the most convenient way to do such procedure?

SNP genome plink merge bed • 290 views
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