Spellman Lab mutation calling pipeline

eagle-i ID

Resource Type

Properties

1. Resource Description

   A GATK-based pipeline for aligning tumor and normal sequencing reads. This perl script programmatically preps and pushes data through a processing pipeline that includes the following tools: BWA mem + SAM tools: Read alignment Picard Tools: Mark duplicates GATK (RealingerTargetCreator, IndelRealinger): Local Realignment GATK (BaseRecalibration and PrintReads): Re-calibrate quality scores

2. Contact

   Peto, Myron, Ph.D.

3. Used by

   Paul Spellman Laboratory

4. Data Input

   FASTQ files from an Illumina Sequencer

5. Data Output

   List of variants found

6. Data Output

   Aligned reads from sequencer (.bam file)

7. Software purpose

   Sequence comparison objective

8. Software purpose

   Sequence alignment objective

9. Website(s)

   http://samtools.sourceforge.net/

10. Related Technique

    Sequencing

11. Developed by

    Peto, Myron, Ph.D.

12. Coded in

    Perl