plink chromosome code
X X chromosome -> 23 Y Y chromosome -> 24 XY Pseudo-autosomal region of X -> 25 MT Mitochondrial -> 26 1-22 autosome -> 1-22
Category: GWAS
PCA with shellfish
Assuming shellfish and all other related software have been installed correctly. Assuming shellfish.py exists then prepare a pbs script, here I called it Shellfish.pbs and I have plink files calledABC.bim ABC.bed ABC.fam cat Shellfish.pbs #!/bin/bash #PBS -N shellfish #PBS -S /bin/bash #PBS -j oe #PBS -l walltime=24:00:00 #PBS -l ncpus=20 #PBS -l mem=100G hostname cd… Continue reading PCA with shellfish
Genomic inflation factor calculation
In GWAS, a common way to investigate if there are any systematic biases that may be present in your association results is to calculate the genomic inflation factor, also known as lambda gc (λgc). The genomic inflation factor λgc is defined as the ratio of the median of the empirically observed distribution of the test statistic… Continue reading Genomic inflation factor calculation
Bioinformatics-Genomics-Genetics 