Java tools for bioinformatics. Tools are not described in detail here see the author's documentation. Note that all tools are compiled though some of them are pretty lab specific or deprecated.

References:

Lindenbaum, Pierre. JVarkit: java-based utilities for Bioinformatics.. http://dx.doi.org/10.6084/m9.figshare.1425030

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

[user@biowulf]$ sinteractive --mem=6g --gres=lscratch:20 salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job

Version 20211013

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID [user@cn3144]$ module load jvarkit/20211013 [user@cn3144]$ cp -L ${JVARKIT_TEST_DATA:-none}/* . [user@cn3144]$ java -jar $JVARKIT_JARPATH/backlocate.jar --help Usage: backlocate [options] Files Options: * -g, --gtf A GTF (General Transfer Format) file. See https://www.ensembl.org/info/website/upload/gff.html . Please note that CDS are only detected if a start and stop codons are defined. -h, --help print help and exit --helpFormat What kind of help. One of [usage,markdown,xml]. -o, --out Output file. Optional . Default: stdout -p, --printSeq print mRNA & protein sequences Default: false * -R, --reference Indexed fasta Reference file. This file must be indexed with samtools faidx and with picard CreateSequenceDictionary --version print version and exit [user@cn3144]$ gc=/fdb/GENCODE/Gencode_human/release_35 [user@cn3144]$ gtf=$gc/gencode.v35.primary_assembly.annotation.gtf [user@cn3144]$ genome=$gc/GRCh38.primary_assembly.genome.fa [user@cn3144]$ echo -e "NOTCH2\tPro1090M\tInteresting" \ | java -jar $JVARKIT_JARPATH/backlocate.jar \ --gtf $gtf -R $genome \ | grep -v "##" \ | java -jar $JVARKIT_JARPATH/prettytable.jar +------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+ | #User.Gene | AA1 | petide.pos.1 | AA2 | transcript.name | transcript.id | transcript.strand | transcript.AA | index0.in.rna | wild.codon | potential.var.codons | base.in.rna | chromosome | index0.in.genomic | exon | messages | extra.user.data | +------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+ | NOTCH2 | Pro | 1090 | Met | NOTCH2 | ENST00000256646.7 | - | P | 3267 | CCA | . | C | chr1 | 119937925 | ENST00000256646.7.Exon20 | . | Interesting | | NOTCH2 | Pro | 1090 | Met | NOTCH2 | ENST00000256646.7 | - | P | 3268 | CCA | . | C | chr1 | 119937924 | ENST00000256646.7.Exon20 | . | Interesting | | NOTCH2 | Pro | 1090 | Met | NOTCH2 | ENST00000256646.7 | - | P | 3269 | CCA | . | A | chr1 | 119937923 | ENST00000256646.7.Exon20 | . | Interesting | +------------+-----+--------------+-----+-----------------+-------------------+-------------------+---------------+---------------+------------+----------------------+-------------+------------+-------------------+--------------------------+----------+-----------------+ [user@cn3144]$ paste <(gunzip -c r1.fastq.gz | paste - - - -) <(gunzip -c r2.fastq.gz | paste - - - -)\ | tr "\t" "\n" \ | java -jar $JVARKIT_JARPATH/fastqjs.jar \ -i -e 'pair.get(0).getReadString().contains("GTTTAAAC") && pair.get(1).getReadString().contains("GTTTAAAC") ' \ > example.fastq [user@cn3144]$ cat <<__EOF__ > filter.js // prints a VARIATION if two samples at least have a DP<200 function myfilterFunction() { var samples=header.genotypeSamples; var countOkDp=0; for(var i=0; i< samples.size();++i) { var sampleName=samples.get(i); if(! variant.hasGenotype(sampleName)) continue; var genotype = variant.genotypes.get(sampleName); if( ! genotype.hasDP()) continue; var dp= genotype.getDP(); if(dp < 200 ) countOkDp++; } return (countOkDp>2) } myfilterFunction(); __EOF__ [user@cn3144]$ java -jar $JVARKIT_JARPATH/vcffilterjs.jar -f filter.js gatk.vcf ... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BLANK NA12878 NA12891 NA12892 NA19238 NA19239 NA19240 chr22 42526449 . T A 151.47 . AC=1;AF=0.071;AN=14;BaseQRankSum=2.662;DP=1226;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=41.2083;MQ=240.47;MQ0=0;MQRankSum=0.578;QD=4.89;ReadPosRankSum=3.611 GT:AD:DP:GQ:PL 0/1:23,8:31:99:190,0,694 0/0:188,0:190:99:0,478,5376 0/0:187,0:187:99:0,493,5322 0/0:247,0:249:99:0,634,6728 0/0:185,0:185:99:0,487,5515 0/0:202,0:202:99:0,520,5857 0/0:181,1:182:99:0,440,5362 chr22 42526634 . T C 32.60 . AC=1;AF=0.071;AN=14;BaseQRankSum=1.147;DP=1225;DS;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=50.0151;MQ=240.65;MQ0=0;MQRankSum=1.151;QD=1.30;ReadPosRankSum=1.276 GT:AD:DP:GQ:PL 0/1:21,4:25:71:71,0,702 0/0:187,2:189:99:0,481,6080 0/0:233,0:233:99:0,667,7351 0/0:230,0:230:99:0,667,7394 0/0:174,1:175:99:0,446,5469 0/0:194,2:196:99:0,498,6239 0/0:174,0:175:99:0,511,5894 chr22 42527793 rs1080989 C T 3454.66 . AC=2;AF=0.167;AN=12;BaseQRankSum=-3.007;DB;DP=1074;DS;Dels=0.01;FS=0.000;HRun=1;HaplotypeScore=75.7865;MQ=209.00;MQ0=0;MQRankSum=3.014;QD=9.36;ReadPosRankSum=0.618 GT:AD:DP:GQ:PL ./. 0/1:72,90:162:99:1699,0,1767 0/1:103,96:202:99:1756,0,2532 0/0:188,0:188:99:0,526,5889 0/0:160,0:160:99:0,457,4983 0/0:197,0:198:99:0,544,6100 0/0:156,0:156:99:0,439,5041 [user@cn3144]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf]$

For version 20240825

In versions≥2023 jvarkit is packaged as a single jar file. Instead of calling applications as java -jar $JVARKIT_JARPATH/<APPLICATION>.jar they are now called with java -jar $JVARKIT_JAR <APPLICATION>. For example:

[user@cn3144]$ module load jvarkit/20240825 [user@cn3144]$ java -jar $JVARKIT_JAR backlocate --help Usage: backlocate [options] Files Options: * -g, --gtf A GTF (General Transfer Format) file. See https://www.ensembl.org/info/website/upload/gff.html . Please note that CDS are only detected if a start and stop codons are defined. -h, --help print help and exit --helpFormat What kind of help. One of [usage,markdown,xml]. -o, --out Output file. Optional . Default: stdout -p, --printSeq print mRNA & protein sequences Default: false * -R, --reference Indexed fasta Reference file. This file must be indexed with samtools faidx and with picard/gatk CreateSequenceDictionary or samtools dict --version print version and exit [user@cn3144]$ gc=/fdb/GENCODE/Gencode_human/release_35 [user@cn3144]$ gtf=$gc/gencode.v35.primary_assembly.annotation.gtf [user@cn3144]$ genome=$gc/GRCh38.primary_assembly.genome.fa [user@cn3144]$ echo -e "NOTCH2\tPro1090M\tInteresting" \ | java -jar $JVARKIT_JAR backlocate \ --gtf $gtf -R $genome \ | grep -v "##"

#!/bin/bash module load jvarkit/20200713 paste <(gunzip -c r1.fastq.gz | paste - - - -) <(gunzip -c r2.fastq.gz | paste - - - -) \ | tr "\t" "\n" \ | java -jar $JVARKIT_JARPATH/fastqjs.jar \ -i -e 'pair.get(0).getReadString().contains("GTTTAAAC") && pair.get(1).getReadString().contains("GTTTAAAC") ' \ > example.fastq

echo -e "NOTCH2\tP1090M\tInteresting" | java -jar $JVARKIT_JARPATH/backlocate.jar --gtf hg19.gtf -R hg19.fa > notch_P1090M echo -e "NOTCH2\tP1090I\tInteresting" | java -jar $JVARKIT_JARPATH/backlocate.jar --gtf hg19.gtf -R hg19.fa > notch_P1090I

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module jvarkit	Loads the jvarkit module for each subjob in the swarm