format bed file

[pierrespc]

Hi,

I am trying to run KINgaroo. I am wondering if the chr info in bed files need to be only numerical or if they can be of format chr like following:

chr1    839494  839495  G   T
chr1    846863  846864  G   C
chr1    851203  851204  G   C
chr1    853088  853089  G   C
chr1    855074  855075  C   G
chr1    858039  858040  C   A
chr1    867551  867552  T   G
chr1    870738  870739  T   G
chr1    871027  871028  A   C
chr1    897324  897325  G   C

because the splitted bed files created are empty and all my alignments and so on are with contig names including chr. If it is not contemplated, I suppose I should just change some function in the script pypackage/kingaroo/KINgaroo/KINgaroo_scripts/helpers.py but before editing your script I would rather confirm there is no trick for this case. Thanks

[DivyaratanPopli]

Hi, chr needs to be numeric in bed file as well as bamfiles. Please refer to README.md for information on input files. I think it's easier to change the input files to numeric chr than editing the script because at different places, the script loops through chromosomes as integers.