When sorting by queryname with Samtools (
samtools sort -n), Samtools does a natural sort by colon-delimited subfield. On the other, when sorty by queryname with Picard (
picard SortSam SORT_ORDER=queryname), Picard does not sort by colon-delimited subfield, instead treating the queryname as one field and then sorting in ASCII sort order (for example, as described in this comment and its sub-comments).
I would like to sort my bam files in the
picard SortSam SORT_ORDER=queryname manner, but Picard SortSam is quite a bit slower than
samtools sort -n;
samtools sort -n can be parallelized while
picard SamSort SORT_ORDER=queryname can't be parallelized. Is there a fast alternative to
picard SamSort SORT_ORDER=queryname for this task?