Scramble: a tool for mobile element insertion detection

Quick Links

Scramble is a mobile element insertion (MEI) detection tool. It identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls.

References:

Rebecca I. Torene, Kevin Galens, Shuxi Liu, Kevin Arvai, Carlos Borroto, Julie Scuffins, Zhancheng Zhang, Bethany Friedman, Hana Sroka, Jennifer Heeley, Erin Beaver, Lorne Clarke, Sarah Neil, Jagdeep Walia, Danna Hull, Jane Juusola, and Kyle Retterer.
Mobile element insertion detection in 89,874 clinical exomes
Genetics in Medicine (2020).

Documentation

Scramble GitHub page

Important Notes

Module Name: Scramble (see the modules page for more information)
Environment variables set
- SCRAMBLE_HOME Scramble installation directory
- SCRAMBLE_BIN Scramble executable directory
- SCRAMBLE_DATA Scramble sample data directory
- If you are using your own reference file make sure you generate *.nhr, *.nin, and *.nsq files using makeblastd as follows:
  module load load ncbi-toolkit
  makeblastdb -in file.fasta -input_type fasta -dbtype nucl

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=4g
salloc.exe: Pending job allocation 56730292
salloc.exe: job 56730292 queued and waiting for resources
salloc.exe: job 56730292 has been allocated resources
salloc.exe: Granted job allocation 56730292
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3148 are ready for job
[user@cn3148 ~]$ module load Scramble 
[+] Loading singularity  3.5.3  on cn3148
[+] Loading Scramble 0.0.20190211.82c78b9  ...

Copy sample data into your current directory:

[user@cn3148 ~]$ cp $SCRAMBLE_DATA/* .

You can run Scramble in two different ways.

1) When you execute the scramble command without arguments, a new shell will be opened for you within a Singularity container:

[user@cn3148 ~]$ scramble
Singularity>

Your environment will change and you will have access to a different set of commands and executables. For example, you can run the command:

Singularity>  Rscript --vanilla /app/cluster_analysis/bin/SCRAMble.R \
                        --out-name ${PWD}/sample.mei.txt \
                        --cluster-file ${PWD}/sample_cluster.txt \
                        --install-dir /app/cluster_analysis/bin \
                        --mei-refs /app/cluster_analysis/resources/MEI_consensus_seqs.fa \
                        --ref /app/validation/test.fa \
                        --eval-dels \
                        --eval-meis \
                        --no-vcf

Running sample: /gpfs/gsfs8/users/apptest2/SCRAMBLE_TEST/sample_cluster.txt 
Running scramble with options:
blastRef : /app/validation/test.fa 
clusterFile : /gpfs/gsfs8/users/apptest2/SCRAMBLE_TEST/sample_cluster.txt 
deletions : TRUE 
indelScore : 80 
INSTALL.DIR : /app/cluster_analysis/bin 
mei.refs : /app/cluster_analysis/resources/MEI_consensus_seqs.fa 
meis : TRUE 
meiScore : 50 
minDelLen : 50 
nCluster : 5 
no.vcf : TRUE 
outFilePrefix : /gpfs/gsfs8/users/apptest2/SCRAMBLE_TEST/sample.mei.txt 
pctAlign : 90 
polyAdist : 100 
polyAFrac : 0.75 
Useful Functions Loaded
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Done analyzing l1 
Done analyzing sva 
Done analyzing alu 
Done analyzing l1 
Done analyzing sva 
Done analyzing alu 
Sample had 0 MEI(s)
Done analyzing MEIs
532 clusters out of 927 were removed due to simple sequence
Number of alignments meeting thresholds: 395 
Number of best alignments: 0 
[1] "Two-End-Deletions: Working on contig 1"
[1] "Two-End-Deletions: Working on contig 10"
[1] "Two-End-Deletions: Working on contig 11"
[1] "Two-End-Deletions: Working on contig 12"
[1] "Two-End-Deletions: Working on contig 13"
[1] "Two-End-Deletions: Working on contig 14"
[1] "Two-End-Deletions: Working on contig 15"
[1] "Two-End-Deletions: Working on contig 16"
[1] "Two-End-Deletions: Working on contig 17"
[1] "Two-End-Deletions: Working on contig 18"
[1] "Two-End-Deletions: Working on contig 19"
[1] "Two-End-Deletions: Working on contig 2"
[1] "Two-End-Deletions: Working on contig 20"
[1] "Two-End-Deletions: Working on contig 22"
[1] "Two-End-Deletions: Working on contig 3"
[1] "Two-End-Deletions: Working on contig 4"
[1] "Two-End-Deletions: Working on contig 5"
[1] "Two-End-Deletions: Working on contig 6"
[1] "Two-End-Deletions: Working on contig 7"
[1] "Two-End-Deletions: Working on contig 8"
[1] "Two-End-Deletions: Working on contig GL000220.1"
[1] "Two-End-Deletions: Working on contig hs37d5"
[1] "Two-End-Deletions: Working on contig X"
[1] "finished one end dels"
Sample had 0 deletions
Done analyzing deletions
Warning message:
In predict.BLAST(bl, seq, BLAST_args = "-dust no") :
  BLAST did not return a match!

Please remember to exit this new shell when you are finished with your session.

Singularity> exit
exit
[user@cn3148]$

2) Alternatively, you can run the Rscript or other command(s) directly from the Linux shell, but in this case the command(s) must be preceded by scramble. For example:

[user@cn3148 ~]$ scramble Rscript --vanilla /app/cluster_analysis/bin/SCRAMble.R \
                        --out-name ${PWD}/sample.mei.txt \
                        --cluster-file ${PWD}/sample_cluster.txt \
                        --install-dir /app/cluster_analysis/bin \
                        --mei-refs /app/cluster_analysis/resources/MEI_consensus_seqs.fa \
                        --ref /app/validation/test.fa \
                        --eval-dels \
                        --eval-meis \
                        --no-vcf

Exit the interactive shell:

[user@cn3148 ~]$ exit
exit
salloc.exe: Relinquishing job allocation 49998864
[user@biowulf ~]$