In this tutorial, we will see how to prepare nominal files from QTLtools for a meta-analysis using the METAL software.
Columns from QTLtools
On the one hand, here are some output columns from QTLtools:
- gene ID (1st column)
- variant ID (8th column)
- p_value (12th column)
- regression slope (14th column)
Columns for METAL
On the other hand, here are the input columns for METAL:
- marker name
- tested allele
- other allele
- p_value
- regression slope / effect
- sample size / weight
Preparation
First, we need to compute the sample size. The phenotype file that QTLtools takes as input is a BED file where the first 6 columns correspond to the chromosome, the start and end positions, the phenotype ID, the phenotype group ID and the strand. The other columns correspond to the individuals:
weight=$(expr $(head -1 gene_expression.bed | tr '\t' '\n' | wc -l) - 6)Then, we need to format the nominal files:
- combine the gene ID with the variant ID to obtain a unique marker name
- extract the tested and other alleles information from the variant ID
- keep the p_value and effect columns as they are
- add a column with the weight computed in the previous step (we will have the same weight for all the markers)
gunzip -c nominal.txt.gz | awk -v awkvar=${weight} 'BEGIN{print "marker""\t""tested""\t""other""\t""p_value""\t""effect""\t""weight"}; {split($8,a,/:/); print $1"_"$8"\t"a[3]"\t"a[4]"\t"$12"\t"$14"\t"awkvar}' > nominal_for_metal.txtConclusion
In conclusion, we need some steps to prepare nominal files from QTLtools for METAL. Is this blog post helpful to you?
