munge-gs type error

[parkjooyoung99]

Hello, I am trying to generate .gs file with 'MAGMA' output and having a trouble.

I sort 'MAGMA' output by zstat with code cut -f 1 prostate_GCST90011808_zscore_file.tsv > gene_symbol.txt paste gene_symbol.txt prostate_GCST90011808.genes.out > test.tsv awk '{print $1, $9}' test.tsv | sort -rn -k 2 | sed 's/ /\t/g' > prostate_GCST90011808_zscorefile.tsv
which gives me output of

With this 'prostate_GCST90011808_zscorefile.tsv', munge-gs always give me the error

What would be the problem,,,,?

I have added my zscorefile converted to 'txt' . Thank you!

prostate_GCST90011808_zscorefile.txt

[KangchengHou]

Thanks for your clear description. There are multiple formatting issue in prostate_GCST90011808_zscorefile.txt.

1. The header should contain GENE, TRAIT, for example:

   GENE    BMI    HEIGHT
   OR4F5   0.001  0.01
   DAZ3    0.01   0.001

2. There are NA entries in GENE column (I recommend to remove them before hand)
3. There is a row (~11093-th rows) with GENE, ZSTAT (maybe some concatenating issue there)

We have added more checking to the zscore / pval files in the master branch. But perhaps it is easier for you for fix these formatting issue in zscorefile before feeding that into munge-gs.

[parkjooyoung99]

Thank you so much. Following your instruction 1 and 2 helped.