Build a DBSNP file from different sources for GATK
Usage: builddbsnp [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
-c, --chromosome
limit to this chromosome
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --out
Output file. Optional . Default: stdout
* -R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard CreateSequenceDictionary
--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 builddbsnp
The java jar file will be installed in the dist
directory.
20200904
The project is licensed under the MIT license.
Should you cite builddbsnp ? 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
$ java -jar dist/depthofcoverage.jar -R src/test/resources/rotavirus_rf.fa src/test/resources/S*.bam 2> /dev/null | column -t
#BAM Sample Contig Length Count Depth
src/test/resources/S1.bam S1 RF01 3302 25037 7.582374318594791
src/test/resources/S1.bam S1 RF02 2687 20275 7.545589877186453
src/test/resources/S1.bam S1 RF03 2592 19583 7.55516975308642
src/test/resources/S1.bam S1 RF04 2362 17898 7.577476714648603
src/test/resources/S1.bam S1 RF05 1579 11887 7.528182393920202
src/test/resources/S1.bam S1 RF06 1356 10201 7.522861356932153
src/test/resources/S1.bam S1 RF07 1074 8115 7.555865921787709
src/test/resources/S1.bam S1 RF08 1059 7980 7.5354107648725215
src/test/resources/S1.bam S1 RF09 1062 7980 7.5141242937853105
src/test/resources/S1.bam S1 RF10 751 5740 7.6431424766977365
src/test/resources/S1.bam S1 RF11 666 5037 7.563063063063063
src/test/resources/S1.bam S1 * 18490 139733 7.557220118983234
src/test/resources/S2.bam S2 RF01 3302 25030 7.580254391278014
src/test/resources/S2.bam S2 RF02 2687 20272 7.544473390398213
src/test/resources/S2.bam S2 RF03 2592 19592 7.558641975308642
src/test/resources/S2.bam S2 RF04 2362 17916 7.585097375105843
src/test/resources/S2.bam S2 RF05 1579 11892 7.531348955034832
src/test/resources/S2.bam S2 RF06 1356 10217 7.534660766961652
src/test/resources/S2.bam S2 RF07 1074 8112 7.553072625698324