How to perform custom annotation using garfield_annotate_uk10k.sh script in GARFIELD tool?

Question

[bk11]

Hi,

I am trying to use the GARFIELD V2 tool (https://www.ebi.ac.uk/birney-srv/GARFIELD/) and create custom annotation data using narrow peak bed files from Roadmap https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidatedImputed/narrowPeak/. GARFIELD provides a script ‘garfield_annotate_uk10k.sh’ to prepare custom annotation data. Unfortunately, the script gives me wrong output per chromosome which looks like following (for every chromosome) with all zero in second column:

My input bed file looks like:

chr1   833927  833927
chr1   1344686 1344686
chr1   17006932     17006932
chr1   20498952    20498952
chr1   21775805          21775805

Output looks like which is not normal:

head chr1

1   33937  0
1   44676 0
1   700693     0
1   498972    0
1   177585          0

Where 0 in the third column represent SNP is not present in my annotation bed file. The normal output file would look like:

1   33937  1
1   44676 0
1   700693     1
1   498972    0
1   177585          1

Where 1 in the third column represent SNP is present in my annotation bed file.

Have any one come across such problem or any one could suggest me way to prepare custom annotation data using narrowPeak bed files from Roadmap (link provided above) as one of input data for GARFIELD. I ll highly appreciate you help.

Thanks

[brantn1]

Hi,

I am running into this same problem when trying to make own custom annotations from the GARFIELD script. Were you able to find a solution for the third column issues? Please let me know!