Sometimes input errors are caused because of non-sorted inputs. Try using these:
- Picard SortSam: Sort SAM/BAM by coordinate or queryname.
- Samtools Sort: Alternate for SAM/BAM, best when used for coordinate sorting only.
- SortBED order the intervals: Best choice for BED/Interval.
- Sort data in ascending or descending order: Alternate choice for Tabular/BED/Interval/GTF.
- VCFsort: Best choice for VFC.
- Tool Form Options for Sorting: Some tools have an option to sort inputs during job execution. Whenever possible, sort inputs before using tools, especially if jobs fail for not having enough memory resources.