- Unique identifier:
- Software type:
- Restrictions to use:
- Input format:
- Output format:
- Computer skills:
- SAMtools, BAMtools, BEDtools, GATK, DBSNP, REFSEQ, PICARD
- Whole Exome Sequencing Analysis Pipeline
- Command line interface
- Input data:
- The raw read data with well-calibrated base error estimates, the reference genome.
- Output data:
- The filtered mapped reads, the recalibrated and realigned BAM files, the paired read information, the predicted SNV calling.
- Operating system:
- Peter Zandi <>
No open topic.
(Pirooznia et al., 2014)
Validation and assessment of variant calling pipelines for next-generation sequencing.
PMID: 25078893 DOI: 10.1186/1479-7364-8-14
Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA; Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, NY, USA; Department of Psychiatry, Carver College of Medicine, University of Iowa School of Medicine, Iowa City, IA, USA; Watson School of Biological Science, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
This project is supported by the NIH funding from R01MH087979, R01MH087992, and K01MH093809.