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Redo / Recalculate gvcf bins

rernstrernst UMC UtrechtMember

Hi GATK Team,

I am wondering whether it is possible to redo the binning of a gvcf. For example if I have a gvcf created with the defaults the gvcf bins are 1 GQ 'wide'. Is it be possible to take this gvcf and redo binning with for example steps of 10.

For example:
Input gvcf:
1 10899 . G <NON_REF> . . END=10899 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,55 1 10900 . A <NON_REF> . . END=10900 GT:DP:GQ:MIN_DP:PL 0/0:2:4:2:0,0,20 1 10901 . G <NON_REF> . . END=10901 GT:DP:GQ:MIN_DP:PL 0/0:4:12:4:0,12,116 1 10902 . G <NON_REF> . . END=10902 GT:DP:GQ:MIN_DP:PL 0/0:4:11:4:0,11,81
Ouput gvcf:
1 10899 . G <NON_REF> . . END=10900 GT:DP:GQ:MIN_DP:PL 0/0:2:5:2:0,6,55 1 10901 . G <NON_REF> . . END=10902 GT:DP:GQ:MIN_DP:PL 0/0:4:12:4:0,12,116

Best,
Robert

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