Using --breakBandsAtMultiplesOf N will ensure that no reference blocks span across
genomic positions that are multiples of N. This is especially important in the
case of scatter-gather where you don't want your scatter intervals to start in the
middle of blocks (because of a limitation in the way -L works in the GATK for VCF
records with the END tag).
For example, running with --breakBandsAtMultiplesOf 5 on this record:
1 69491 . G <NON_REF> . . END=69523 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
Will produce the following records:
1 69491 . G <NON_REF> . . END=69494 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
1 69495 . C <NON_REF> . . END=69499 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
1 69500 . T <NON_REF> . . END=69504 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800
etc.
Added docs and a new test.
ea8a1edeb6