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BED File from COSMIC Mutation

I am took mutations from cosmic and converted them into bed file but I don't know if its correct bed file or not

chrX    18622145    18622146    CDKL5   SO:0001583
chrX    18616686    18616687    CDKL5   SO:0001583
chrX    18622958    18622959    CDKL5   SO:0001583
chrX    18646617    18646618    CDKL5   SO:0001583
chrX    18600018    18600019    CDKL5   SO:0001583
chrX    18627618    18627619    CDKL5   SO:0001583
chrX    18622811    18622812    CDKL5   SO:0001583
chrX    18622978    18622979    CDKL5   SO:0001583
chrX    18622581    18622582    CDKL5   SO:0001583
chrX    18671607    18671608    CDKL5   SO:0001583
chrX    18525250    18525251    CDKL5   SO:0001583
chrX    18593494    18593495    CDKL5   SO:0001583
chrX    18593503    18593504    CDKL5   SO:0001583
chrX    18593566    18593567    CDKL5   SO:0001583
chrX    18593568    18593569    CDKL5   SO:0001583
chrX    18600027    18600028    CDKL5   SO:0001583
chrX    18600051    18600052    CDKL5   SO:0001583
chrX    18627663    18627664    CDKL5   SO:0001583
chrX    18528969    18528970    CDKL5   SO:0001583
chrX    18606105    18606106    CDKL5   SO:0001583
chrX    18606220    18606221    CDKL5   SO:0001583
chrX    18664153    18664154    CDKL5   SO:0001583
chrX    18606092    18606093    CDKL5   SO:0001583
chrX    18668711    18668712    CDKL5   SO:0001583
chrX    18622638    18622639    CDKL5   SO:0001583
chrX    18646664    18646665    CDKL5   SO:0001583
chrX    18638036    18638037    CDKL5   SO:0001583
chrX    18616729    18616730    CDKL5   SO:0001583
chrX    18664180    18664181    CDKL5   SO:0001583
chrX    18616668    18616669    CDKL5   SO:0001583
chrX    18643337    18643338    CDKL5   SO:0001583
chrX    18646511    18646512    CDKL5   SO:0001583
chrX    18606127    18606128    CDKL5   SO:0001583
chrX    18602448    18602449    CDKL5   SO:0001583
chrX    18626963    18626964    CDKL5   SO:0001583
chrX    18643316    18643317    CDKL5   SO:0001583
chrX    18631387    18631388    CDKL5   SO:0001583
cosmic
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updated by michael.ante michael.ante • written by anasjamshed anasjamshed

1 answer

Hi according to the file format which is explained here, the 5th column should be a score (between 1 and 1000 - or a '.' ). Usually, you have 3, 4, 6 or 12 columns, depending on your requirements.

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written by michael.ante michael.ante

I took mutation from cosmic

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written by anasjamshed anasjamshed

Depending on what you want to do with that it, your file might work:

bedtools sort -i biostars_cosmic.bed
chrX    18525250        18525251        CDKL5   SO:0001583
chrX    18528969        18528970        CDKL5   SO:0001583
chrX    18593494        18593495        CDKL5   SO:0001583
chrX    18593503        18593504        CDKL5   SO:0001583
...

If you want to load it into IGV, it might break, since it expects the strand and a score.

Without more information on what you are trying to achieve, we cannot help you further.

• 0 views • link
written by michael.ante michael.ante

I want to intersect it with ClinVar mutation file

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written by anasjamshed anasjamshed

I'd try it with a subset, you can verify IGV (or any other Genome Viewer) and look if it delivers meaningful results.

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written by michael.ante michael.ante

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