Description
Splits a SAM/BAM/CRAM file to multiple files. This tool splits the input query-grouped SAM/BAM/CRAM file into multiple files while maintaining the sort order. This can be used to split a large unmapped input in order to parallelize alignment.
Input
Split to have approximately N reads per output file, e.g. 4000000
.
The actual number of reads per output file will vary by no more than the number of output files * (the maximum number of reads with the same queryname - 1).
Incompatible with split_to_N_files
Tools
picard Documentation
Splits a SAM or BAM file to multiple BAMs by number of reads.