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DepthOfCoverage interval_summary +1 on the start position of each intervals

Hi,

When I check the coordinates of intervals given by DepthOfCoverage "*.interval_summary" file, I found that it tried to add one on the start position of each intervals. For example, the original coordinates in my .bed interval file is 3669022-3669474, then the DOC will give 3669023-3669474, only the start position, not the end one, actually.

I am not sure whether this is caused by "start from 0" or "start from 1" problem, because I have no idea about the coordinates in my original bed files start from 1 or start from 0.

I just worry does GATK DOC will miss one base for each interval?

bless~
XL

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  • liuxingliangliuxingliang SingaporeMember

    @Geraldine_VdAuwera said:
    That is the expected behavior when you use a bed file. If it's not what you want, you can either adjust your bed intervals or convert your bed file to a .list file.

    Hi,

    May I know why GATK will increase one on the start position, but not increase on the end position?

    bless~
    XL

  • liuxingliangliuxingliang SingaporeMember

    @Geraldine_VdAuwera said:
    That is the expected behavior when you use a bed file. If it's not what you want, you can either adjust your bed intervals or convert your bed file to a .list file.

    Hi Geraldine,

    Thank you for your help. I think I know why already. After checking the interval file format for GATK, I know that GATK expect a picard format interval list, which is 1-based close (include start and end both), however, BED format is 0-based open (only include start, but exclude end), that's why GATK only increase 1 on my start postions of BED file.

    bless~
    XL

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