HG38 reference
Song Cao, Reyka Jayasinghe, Qingsong Gao, Mike Wendl
Pipeline for discovering splice-site creating mutations (SCMs) from RNA-Seq
Please cite the following paper if you use MiSplice pipeline:
Systematic Analysis of Splice-Site-Creating Mutations in Cancer
Jayasinghe RG*, Cao S*, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang W, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, The Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L, Cell Rep 2018 Apr 3;23(1):270-281
Usage: perl misplice.pl --rdir run_folder --bed bed_file --ref ref_file --q q_name --step <step_numuber>
<run_folder> = full path of the folder holding mutation annotation file (maf) file for all mutations (misplice.input.maf) and file for the sample list (currently named as Samples).
<bed_file> bed file for HG38 refernece: please follow ./resource/GRCh38/work_log_gtf to generate it or download from https://drive.google.com/file/d/1M2yLLjxBwOjUOu-uIxwtUrD_DHTTpioJ/view?usp=sharing
<ref_file> HG38 refernece file
<q_name> which bsub quenue for submitting job
<step_number> run this pipeline step by step (Either run step 1 to step 9 separately) OR run step 11, then steps 7,8,9 separately.
[1] Split mutation annotation file (MAF) into multiple files for processing
[2] Run discovery step of mutation induced splice creating events
[3] Generate control MAF
[4] Calculate number of supporting reads for control samples
[5] Combine the read count for case and control samples
[6] Calculate the splice score (MaxEntScan)
[7] Split novel sites for bam readcounts
[8] Do bam readcounts
[9] Run rc, hla and expression filtering
File format for input MAF (shortened):
1 GENE VPS13D
2 CHR 1
3 START 12418559
4 STOP 12418559
5 STRAND +
6 MUTATION TYPE Missense_Mutation
7 TYPE SNP
8 REFALLELE C
9 TUMORALLELE1 T
10 TUMORALLELE2 T
11 TUMOR SAMPLE TCGA-02-0047-01A-01D-1490-08
12 NORMAL SAMPLE TCGA-02-0047-10A-01D-1490-08
13 CANCER TYPE gbm
File format for samples as following (table-delimited with sample id and cancer type): TCGA-02-0047 gbm
TCGA-02-0055 gbm
TCGA-02-2483 gbm
TCGA-02-2485 gbm
TCGA-02-2486 gbm