Hi everyone, I'm digging into gatk best practice wdl to speed it up a little bit and would like to scatter BQSR into an even intervals. Currently default task for intervals generation split the genome into uneven parts (chromosome based intervals basically) https://github.com/broadinstitute/warp/blob/c6c8cbd947fe898310ad83072c1aeb757a72e182/tasks/broad/UnmappedBamToAlignedBam.wdl#L193:~:text=scatter%20(subgroup%20in%20CreateSequenceGroupingTSV.sequence_grouping)%20%7B

`chr1:1+

chr2:1+

chr3:1+

chr4:1+

chr5:1+

chr6:1+

chr7:1+

chr8:1+

chr9:1+

chr10:1+

chr11:1+

chr12:1+ chr13:1+

chr14:1+ chr15:1+

chr16:1+ chr17:1+

chr18:1+ chr19:1+ chr20:1+

chr21:1+ chr22:1+

chrX:1+ chrY:1+ chrM:1+ _and all unmapped here_ `

I'd like to change the task CreateSequenceGroupingTSV so it would produce even interval with given length (let say all genome into 15 shard plus additional shard for unmapped sequences)

Is it a reasonable approach? I do not see any specific reasons to have uneven intervals, which eventually transform into different execution time between shards. For me it looks like I can optimize that step, but I assume that someone already thought about it and for some reasons did not implement it into gatk production version, which is suspicious. Therefore, I really appreciate a second opinion on that

Best, Eugene