Creating instrumental variable for mendelian randomisation - in Ubuntu

[rmgpanw]

Problem summary

• Hi, I'm trying to create an instrumental variable for age-related macular degeneration (AMD). I have downloaded summary data for the following study https://www.ebi.ac.uk/gwas/studies/GCST003219
• Sample of data shown below:

Marker	Chrom	Pos	Allele1	Allele2	Ncases	Ncontrols	GC.Pvalue	Overall
rs12083781	1	796375	C	T	16144	17832	0.0829	+
rs75932129	1	796767	A	G	16144	17832	0.101	-
rs58013264	1	797440	C	T	16144	17832	0.0836	+
rs10900604	1	798400	G	A	16144	17832	0.0967	+
rs11240777	1	798959	A	G	16144	17832	0.102	+
rs61768212	1	801467	C	G	16144	17832	0.0846	+
rs7553096	1	802026	A	G	16144	17832	0.0787	+
rs10157494	1	802496	T	C	16144	17832	0.103	+
rs7526310	1	804759	T	C	16144	17832	0.0799	+

or download here: sample.txt

• I would like to filter filter for only those SNPs with a 'GC.Pvalue' of significance p < 0.00001

I have tried the following, which does not work

awk -F '{if ( $8 = 0.0000.) print $0 }' sample.txt

I get 'syntax error' when I run this with the sample.txt file

Could someone please advise me on how to improve on this? Thanks!

[alhenry]

I think there are a couple of things that caused syntax errors in the initial code:

• -F (field separator) option needs to be followed by an argument. However, I think this can be omitted as the default is whitespace so tab / space should be fine.
• = operator should be < (or == for "equal to", but that's not what we want)
• 0.0000. should be 0.00001

The following should work:
awk '$8 < 0.00001' sample.txt

(it wont show any output as there is no variant with P < 0.00001, so to check you can change it to e.g. awk '$8 < 0.1' sample.txt

If you want to preserve the header: awk 'NR==1 || $8 < 0.1' sample.txt