User manual
Usage:
perl sr_inversion.pl [options]
Options:
-h,--help
Print a brief help message and exits.
-m,--man
Prints the manual page and exits.
-i,--input
Input bam file (Required)
-o,--outpre
Prefix of output file (Required)
-s,--scenario
Which scenario to use (Required): scenario 1: inversion
partially covered by read scenario 2: inversion completely
covered by read
-t,--step
Which step to run only (all steps will be processed by default):
step1: Extract low quality reads step2: Split reads step3:
re-map splitted reads step4: Select candidate reads step5:
Detect inversion regions step6: Combine inversion regions
-c,--chr
Limited on which chromosome, all chromosomes (1..2,X,Y,M) will
be used by default.
-b,--bwa
Location of BWA for mapping
-l,--samtools
Location of samtools for bam/sam files handling
-r,--reference
Location of references in FASTA format (Required)
-k,--keep
Keep all intermediate files. (Will generate large files, caution
when using whole genome high-coverage data>
-p,--path
Path of libraries.
-cp,--clip
Only reads with longer than #bp clipped ends will be included
for scenario 1 [10]
-g,--gap
#bp gap length for sliding window to move on each time when
splitting reads [1]
-m,--match
Only select exact matched reads
-mw,--minwin
minimum window size for invertion in each read in scenario 2 [5]
-mi,--maxinv
maximum inversion to be included for scenario 1 [1000]
Example:
Scenario 1: perl SRinversion.pl -i chr20.bam -o sen1 -s 1 -c 20 -r chr20.fa --keep
Scenario 2: perl SRinversion.pl -i chr20.bam -o sen2 -s 2 -c 20 -g 5 -r chr20.fa --keep