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FATBAM [0.9.9b-31/05/2018]
FATBAM clipping & coverage on amplicons
Antony Le Bechec @ IRC © GNU-GPL
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Requirements
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Reference genome (e.g. hg19.fa)
PICARD >=1.95
SAMTOOLS >=1.2
BEDTOOLS >=2.17
JAVA >=1.8
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Usage example
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Clipping
./FATBAM.clipping.sh --bam=examples/sample.aligned.unclipped.bam --output=examples/sample.aligned.clipped.bam --manifest=examples/sample.manifest -v;
Coverage
./FATBAM.coverage.sh --bam=examples/sample.aligned.clipped.bam --output=examples/sample.aligned.clipped.bam.coverage --manifest=examples/sample.manifest -v;
column -t examples/sample.aligned.clipped.bam.coverage;
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FATBAMClipping [0.9.3b-11/05/2018]
FATBAM clipping
Antony Le Bechec @ IRC © GNU-GPL
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RELEASE NOTES:
0.9b-30/05/2016: Script creation
0.9.1b-01/06/2016: Deletion of temporary files
0.9.2b-02/06/2016: Few bugs corrected
0.9.3b-11/05/2018: Temporary files in a temporary folder. Few bugs fixed.
USAGE: FATBAM.clipping.sh --bam= --manifest= --output= [options...]
-b/--bam Aligned SAM/BAM file (mandatory)
-m/--manifest MANIFEST file (mandatory)
-c/--chr Filter reads on chromosome (defaut all reads)
-a/--clipping_options Clipping options
-o/--output Clipped Aligned BAM file (defaut *clipped.bam)
-e/--env ENVironment file
-r/--ref REFerence genome
-p/--picardlib PICARD Library (disabled if ENV)
-s/--samtools SAMTOOLS (disabled if ENV)
-l/--bedtools BEDTOOLS (disabled if ENV)
-t/--tmp Temporary folder option (default /tmp)
-u/--threads number of threads for multithreading and samtools option (default 1)
-z/--compress compress level samtools option, from 0 to 9 (default 0)
-x/--multithreading Multithreading option (default false, need make installed)
-v/--verbose VERBOSE option
-d/--debug DEBUG option
-n/--release RELEASE option
-h/--help HELP option
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FATBAMCoverage [0.9.3b-31/05/2017]
FATBAM coverage calculation on amplicons
Antony Le Bechec @ IRC © GNU-GPL
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RELEASE NOTES:
0.9b-02/06/2016: Script creation
0.9.1b-28/03/2017: Bug fixed on output if no primers defined
0.9.2b-11/05/2017: Temporary files in a temporary folder. Bug fixed.
0.9.3b-31/05/2017: Multithreading. Bug fixed.
USAGE: FATBAM.coverage.sh --bam= --manifest= --output= [options...]
-b/--bam Aligned and clipped BAM file (mandatory)
-m/--manifest MANIFEST file (mandatory)
-s/--unclipped Indicates if the BAM file is NOT clipped (yet) (default: 0/FALSE, means that the BAM IS clipped)
-c/--chr Filter reads on chromosome (defaut all reads)
-o/--output Coverage file from Aligned BAM file depending on Manifest (defaut BAM.coverage)
-e/--env ENVironment file
-r/--ref REFerence genome
-p/--picardlib PICARD Library (disabled if ENV)
-i/--picard PICARD JAR (disabled if ENV)
-s/--samtools SAMTOOLS (disabled if ENV)
-l/--bedtools BEDTOOLS (disabled if ENV)
-j/--java JAVA (disabled if ENV, default 'java')
-t/--tmp Temporary folder option (default /tmp)
-u/--threads number of threads for multithreading and samttols option (default 1)
-x/--multithreading Use multithreading (default FALSE)
-v/--verbose VERBOSE option
-d/--debug DEBUG option
-n/--release RELEASE option
-h/--help HELP option