picard

picard ReorderSam

picard ReorderSam

Version:
2.20.x
Identifier: TL_e24fa5_36.c8
Tool

Description


Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. Runs substantially faster if the input is an indexed BAM file.

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