ReadSort

ReadSort is a Hadoop utility to sort read alignments. Currently ReadSort only supports sorting by mapped coordinate, and only supports reading and writing SAM.

Currently ReadSort is tuned to work well sorting mappings uniformly distributed over the reference.

ReadSort works by breaking up the output into several several sorted parts, one per reduce task (like all Hadoop applications). Each output file is itself sorted. In addition, all mappings in part n come before part n+1. Therefore, to create a single file with all the ordered data one merely has to concatenate all the output files in order.

Sorting using ReadSort requires access to the annotations file of the reference used to create the mappings (because ReadSort has to read the relative positions of the contigs).

Usage

Creating a single sorted SAM requires two steps: sorting and merging.

1. seal read_sort -ann file:///references/human_g1k.ann hdfs_input_sam hdfs_sorted
2. seal merge_alignments --sort-order coordinate -ann file:///references/human_g1k.ann hdfs_sorted > local_sorted.sam

Alternatively, you can place the sorted output directly on HDFS:

seal merge_alignments --sort-order coordinate -ann file:///references/human_g1k.ann hdfs_sorted whole_sorted.sam

You could also convert it to bam, on-the-fly:

seal merge_alignments --sort-order coordinate -ann file:///references/human_g1k.ann hdfs_sorted | samtools view -bST  /references/human_g1k.fai /dev/stdin -o whole_sorted.bam

You can also add the read group header to the SAM. Run ./bin/merge_alignments --help to see the options.

Remember that the annotation file path must be accessible by all Hadoop cluster nodes. It will be accessed by the mappers and partitioners. You may place the file on a shared volume or HDFS. Also, unqualified paths (without file://) are assumed to be on the Hadoop cluster’s default file system (usually HDFS).

seal read_sort follows the normal Seal usage convention. See the section Program Usage for details.

Distributed reference

Option: --distributed-reference, -distref

ReadSort also supports using a distributed reference archive, much like Seqal. In fact, this approach may prove advantageous if you call ReadSort right after aligning with Seqal since Hadoop may be able to reuse the archive it distributed in the previous step.

To use this feature, specify the name of the reference archive to be distributed with -distref, then use -ann to specify the name of the annotations file relative to the archive root.

Note that you will still need a locally accessible annotations file for the merging step.

Configurable Properties

ReadSort does not have any program-specific configurable properties at the moment. You can still use its section to configure Hadoop property values specific to ReadSort.

Note

Config File Section Title: ReadSort