vcf-split keeps breakends together, but I thought it would just keep them in the same file. In practice, it moves the records around and breaks the file sorting.
So, for example, records:
III 3226364 MantaDEL:78744:0:0:0:0:0
III 3228674 MantaBND:78991:0:1:1:0:0:1
III 3228676 MantaBND:78991:0:1:0:1:0:1
III 3228678 MantaINS:78991:0:0:0:0:0
III 3228681 MantaDEL:78991:0:0:0:0:1
III 3228782 MantaBND:78991:0:1:0:1:0:0
III 3228783 MantaBND:78991:0:1:1:0:0:0
become:
III 3226364 MantaDEL:78744:0:0:0:0:0
III 3228678 MantaINS:78991:0:0:0:0:0
III 3228681 MantaDEL:78991:0:0:0:0:1
III 3228674 MantaBND:78991:0:1:1:0:0:1
III 3228676 MantaBND:78991:0:1:0:1:0:1
III 3228782 MantaBND:78991:0:1:0:1:0:0
III 3228783 MantaBND:78991:0:1:1:0:0:0
Is there any reason why this behavior?
Would it make sense to add an option to keep the records sorted?
vcf-split
keeps breakends together, but I thought it would just keep them in the same file. In practice, it moves the records around and breaks the file sorting.So, for example, records:
become:
Is there any reason why this behavior? Would it make sense to add an option to keep the records sorted?
thanks,