IMPACT-Pipeline: MSK-IMPACT assay data analysis framework to process data on LSF/SGE¶
Author: | Ronak H Shah, Donavan Cheng, Ahmet Zehir, Aijazuddin Syed, Raghu Chandramohan, Meera Prasad et.al |
---|---|
Contact: | rons.shah@gmail.com |
Source code: | http://github.com/rhshah/IMPACT-Pipeline |
License: | Apache License 2.0 |
IMPACT-Pipeline is a Perl/Python/R command-line software toolkit to process data, call somatic aberrations (SNV,INDELS,SV,CNV) generated by NGS based MSK-IMPACT assay. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina.
Contents:
- Installation
- Requirements
- Usage
- Description of sub-scripts
- File Description
- QC Metrics Files
- Proj_*_All_Metrics.pdf
- Proj_*_ALL_basequalities.txt
- Proj_*_ALL_Canonical_exoncoverage.txt
- Proj_*_ALL_exoncoverage.txt
- Proj_*_ALL_exonnomapqcoverage.txt
- Proj_*_ALL_FPavgHom.txt
- Proj_*_ALL_FPCResultsUnMatch.txt
- Proj_*_ALL_FPCResultsUnMismatch.txt
- Proj_*_ALL_FPCsummary.txt
- Proj_*_ALL_FPhet.txt
- Proj_*_ALL_FPsummary.txt
- Proj_*_ALL_gcbias.txt
- Proj_*_ALL_genecoverage.txt
- Proj_*_ALL_genotypehotspotnormals.txt
- Proj_*_ALL_HSmetrics.txt
- Proj_*_ALL_insertsizemetrics.txt
- Proj_*_ALL_intervalnomapqcoverage_loess.txt
- Proj_*_ALL_intervalnomapqcoverage.txt
- Proj_*_ALL_orgbasequalities.txt
- Copy Number Files
- Structural Variant Files
- Per Sample Files
- s_*_Proj_*_copynumber.seg
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.canonical.exon.covg.sample_interval_summary
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.gene_nomapq.covg.sample_interval_summary
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.gene.covg.sample_interval_summary
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.target.covg
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.tiling_nomapq.covg.sample_interval_summary
- s_*_Proj_*_mrg_cl_aln_srt_MD_IR_BR.tiling.covg.sample_interval_summary
- Sample Info File
- Variant Files
- annotated_exonic_variants.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotated.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedExonic.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedExonic.Dropped.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedExonic.Filtered.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedSilent.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedSilent.Dropped.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedSilent.Filtered.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelExonic.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelExonic.Dropped.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelExonic.Filtered.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelSilent.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelSilent.Dropped.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotatedNonPanelSilent.Filtered.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_annovarAnnotated_All_Filtered.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth.txt
- Proj_*_AllSomaticMutIndel_withAlleleDepth_mergedDNP.txt
- QC Metrics Files
Citation¶
If you use this software in a publication, please cite our paper