paired-end bam clip bases outside insert range
Usage: biostar480685 [options] Files
Options:
--bamcompression
Compression Level.
Default: 5
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
-R, --reference
For reading/writing CRAM files. Indexed fasta Reference file. This file
must be indexed with samtools faidx and with picard
CreateSequenceDictionary
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew biostar480685
The java jar file will be installed in the dist
directory.
20201223
The project is licensed under the MIT license.
Should you cite biostar480685 ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
input must be sorted on read name using samtools sort -n
or ` samtools collate`
samtools collate -O input.bam| java -jar dist/biostar480685.jar