MINTIE: identifying novel, rare transcriptional variants in cancer RNA-seq data

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MINTIE is a tool for identifying novel, rare transcriptional variants in cancer RNA-seq data. MINTIE detects gene fusions, transcribed structural variants, novel splice variants and complex variants, and annotates all novel transcriptional variants.

References:

Marek Cmero, Breon Schmidt, Ian J. Majewski, Paul G. Ekert, Alicia Oshlack & Nadia M. Davidson
MINTIE: identifying novel structural and splice variants in transcriptomes using RNAseq data
Genome Biology, (2021) 22:296; https://doi.org/10.1186/s13059-021-02507-8

Documentation

Important Notes

Module Name: MINTIE (see the modules page for more information)
Unusual environment variables set
- MINTIE_HOME installation directory
- MINTIE_BIN executable directory
- MINTIE_DATA sample data directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=16g -c 16 --gres=lscratch:20
[user@cn3335 ~]$module load MINTIE 
[+] Loading java 12.0.1  ...
[+] Loading MINTIE 0.4.2 ...
[user@cn3335 ~]$ mkdir -p /data/$USER/MINTIE && cd /data/$USER/MINTIE

Produce testing data:

[user@cn3335 ~]$mintie -t

and run mintie on the these data:

[user@cn3335 ~]$ mintie -w -p test_params.txt cases/*.fastq.gz controls/*.fastq.gz   
????????????????????????????????????????????????????????????????????????????????????????????????????
|                              Starting Pipeline at 2022-12-02 13:05                               |
????????????????????????????????????????????????????????????????????????????????????????????????????

================================ Stage fastq_dedupe (allvars-case) =================================
...
==================================== Stage trim (allvars-case) =====================================
...
================================== Stage assemble (allvars-case) ===================================
...
============================= Stage create_salmon_index (allvars-case) =============================
...
================================= Stage run_salmon (allvars-case) ==================================
...
================================ Stage run_salmon (allvars-control) ================================
...
=========================== Stage create_ec_count_matrix (allvars-case) ============================
...
=================================== Stage run_de (allvars-case) ====================================
...
========================== Stage filter_on_significant_ecs (allvars-case) ==========================
...
======================== Stage align_contigs_against_genome (allvars-case) =========================
...
============================= Stage sort_and_index_bam (allvars-case) ==============================
...
============================== Stage annotate_contigs (allvars-case) ===============================
...
=============================== Stage refine_contigs (allvars-case) ================================
...
================================ Stage calculate_VAF (allvars-case) ================================
...
================================ Stage post_process (allvars-case) =================================
index file allvars-case/novel_contigs.fasta.fai not found, generating...

======================================== Pipeline Succeeded ========================================
20:30:00 MSG:  Finished at Tue Jul 25 20:30:00 EDT 2023
20:30:00 MSG:  Outputs are:
                allvars-case/vaf_estimates.txt
                allvars-case/allvars-case_results.tsv
                allvars-case/novel_contigs.bam
                allvars-case/novel_contigs.vcf
                allvars-case/all_fasta_index/allvars-case.fasta (pre-existing)
                ... 4 more ...
[user@cn3335 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$