Difference between revisions of "Samblaster"
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 21:24, 6 December 2019
Description
samblaster is a fast and flexible program for marking duplicates in read-id sorted paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.
When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Required Modules
Serial
- samblaster
System Variables
- HPC_SAMBLASTER_DIR - installation directory
- HPC_SAMBLASTER_DIR - executable directory
Validation
- Validated 4/5/2018