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## ***Powerpoint slides for this workshop: Workshop_mtDNA_QC_analysis.pptx
Please download all files and create a folder on your PC or cluster to run the analysis. Remember: plink must be stored in the same folder if running on your PC.
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Homoplasmic and common variants filtering using PLINK in the SCC cluster
module load bio/PLINK2/20210420-x86_64 |
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Merged.vcf.gz --double-id --max-alleles 2 --vcf-half-call haploid --make-bed --out |
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Workshop_samples-05-17-23 |
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#NOTE: After running the command above you need to ensure that you got 4 different files called file_name_output Workshop_samples-05-17-23.bed, file_name_output Workshop_samples-05-17-23.bim, file_name_output Workshop_samples-05-17-23.fam and file_name_output.log. Workshop_samples-05-17-23.log.
awk '{print $1, $1'MT-'$4, $3, $4, $5, $6}' Workshop_samples-05-17-23.bim > Workshop_samples-05-17-23_nv.bim |
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