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In this step, we will process BAM files from previous step to resolve splice alignments. GATK is strict about chromosome order, and thus we include preventative re-sorting steps using Picard-ReorderSAM app.
Input Data:
| Input | Description | Example |
|---|---|---|
| BAM files | BAM files with uniquely mapped reads | iplantcollaborative > example_data > HAMR_tutorial -> unique_mapping_reads_assignRG -> output.RG.bam |
RUN Picard-ReorderSAM
- Click on "Apps" tab in the Discovery Environment and search for "Picard-ReorderSAM".
- Under Input section, provide input BAM file (output from Picard-AddOrReplaceReadGroups). Provide Reference sequence, dictionary and index files from the tutorial example data (iplantcollaborative > example_data > HAMR_tutorial -> reference_genome). Reference dict for your genome can be generated using GATK-CreateSequenceDictionary app.
- Provide an output file name or leave it to defaults and launch analysis.
Splits reads that contain Ns in their cigar string using GATK-SplitNCigarReads
- Search for "GATK-SplitNCigarReads v3.5" from the app tab. Click on the app icon.
- Provide Reference sequence, dictionary and index files from the tutorial example data. Input reordered BAM and index file from the previous step. Example data for this step is provided at iplantcollaborative > example_data > HAMR_tutorial -> reordered_BAM_files.
- Provide an output file name or leave it to defaults and launch analysis.
Output/Results
| Output | Description | Example |
|---|---|---|
| BAM file | BAM file with reads split at N CIGAR elements and CIGAR strings updated. | iplantcollaborative > example_data > HAMR_tutorial -> resolved_splice_alignments |
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