Read and Print a Tab Separated File Java

jvarkit

Sam2Tsv

Last commit

Prints the SAM alignments every bit a TAB delimited file.

Usage

            Usage: sam2tsv [options] Files   Options:     -h, --help       impress help and go out     --helpFormat       What kind of assistance. 1 of [usage,markdown,xml].     -o, --output       Output file. Optional . Default: stdout     -R, --reference       Indexed fasta Reference file. This file must be indexed with samtools        faidx and with picard CreateSequenceDictionary     --regions       Limit analysis to this interval. A source of intervals. The post-obit        suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz,        gtf.gz.Otherwise information technology could exist an empty string (no interval) or a list of        manifestly interval separated by '[ \t\due north;,]'     -Northward, --skip-N       Skip 'Due north' operator       Default: simulated     --validation-stringency       SAM Reader Validation Stringency       Default: LENIENT       Possible Values: [STRICT, LENIENT, SILENT]     --version       print version and go out

Keywords

sam
bam
table
cram
tsv

See too in Biostars

https://www.biostars.org/p/157232
https://world wide web.biostars.org/p/59647
https://world wide web.biostars.org/p/253828
https://www.biostars.org/p/264875
https://www.biostars.org/p/277493

Compilation

Requirements / Dependencies

java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/bug/23 )

Download and Compile

                          $              git clone              "https://github.com/lindenb/jvarkit.git"              $                            cd              jvarkit              $              ./gradlew sam2tsv

The java jar file volition be installed in the dist directory.

Cosmos Date

20170712

Source code

https://github.com/lindenb/jvarkit/tree/master/src/primary/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/principal/src/test/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2TsvTest.java

Contribute

Upshot Tracker: http://github.com/lindenb/jvarkit/bug
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite sam2tsv ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.physician

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

Example

            $  coffee -jar dist/sam2tsv.jar -R src/test/resources/toy.fa src/test/resources/toy.bam    #Read-Name  Flag  MAPQ  CHROM  READ-POS0  READ-Base  READ-QUAL  REF-POS1  REF-Base  CIGAR-OP r001        163   thirty    ref    0          T          .          7         T         M r001        163   30    ref    1          T          .          8         T         M r001        163   30    ref    ii          A          .          9         A         Grand r001        163   30    ref    3          G          .          ten        G         One thousand r001        163   thirty    ref    four          A          .          11        A         1000 r001        163   30    ref    5          T          .          12        T         M r001        163   xxx    ref    6          A          .          thirteen        A         G r001        163   30    ref    7          A          .          xiv        A         Chiliad r001        163   30    ref    8          A          .          .         .         I r001        163   30    ref    9          G          .          .         .         I r001        163   30    ref    10         A          .          .         .         I r001        163   30    ref    11         One thousand          .          .         .         I r001        163   30    ref    12         G          .          15        K         K r001        163   30    ref    13         A          .          sixteen        A         M r001        163   30    ref    fourteen         T          .          17        T         M r001        163   thirty    ref    15         A          .          18        A         Grand r001        163   30    ref    .          .          .          19        G         D r001        163   thirty    ref    sixteen         C          .          20        C         Grand r001        163   xxx    ref    17         T          .          21        T         Thou r001        163   30    ref    eighteen         Grand          .          22        Grand         G r002        0     30    ref    0          A          .          8         T         Southward r002        0     xxx    ref    1          A          .          .         .         I r002        0     xxx    ref    2          A          .          .         .         I r002        0     thirty    ref    three          A          .          9         A         Thou r002        0     30    ref    4          G          .          10        Grand         M r002        0     30    ref    5          A          .          11        A         M r002        0     30    ref    half dozen          T          .          12        T         M r002        0     30    ref    vii          A          .          thirteen        A         1000 r002        0     30    ref    eight          A          .          14        A         Chiliad r002        0     thirty    ref    .          .          .          .         .         P r002        0     thirty    ref    9          One thousand          .          .         .         I r002        0     thirty    ref    .          .          .          .         .         P r002        0     30    ref    10         G          .          .         .         I r002        0     30    ref    xi         G          .          fifteen        M         G r002        0     xxx    ref    12         A          .          16        A         M (...)

Example 2

sam2tsv tin can read data from a linux pipe.

            samtools view -h input.bam | coffee -jar dist/sam2tsv.jar

Citations

Sam2tsv was cited in :

"Illumina TruSeq Synthetic Long-Reads Empower De Novo Associates and Resolve Circuitous, Highly-Repetitive Transposable Elements" . McCoy RC, Taylor RW, Blauwkamp TA, Kelley JL, Kertesz M, et al. (2014) Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements. PLoS ONE 9(9): e106689. doi: ten.1371/journal.pone.0106689 http://journals.plos.org/plosone/article?id=ten.1371/periodical.pone.0106689
"High-Throughput Identification of Genetic Variation Affect on pre-mRNA Splicing Efficiency". Scott I Adamson, Lijun Zhan, Brenton R Graveley. doi: https://doi.org/10.1101/191122.
"Linkage of A-to-I RNA editing in metazoans and the touch on genome development " Molecular Biology and Development, msx274, https://doi.org/x.1093/molbev/msx274
"Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency" Genome Biology201819:71 https://doi.org/ten.1186/s13059-018-1437-x
"Accurate detection of m6A RNA modifications in native RNA sequences" Huanle Liu, Oguzhan Begik, Morghan C Lucas, Christopher E Mason, Schraga Schwartz, John S Mattick, Martin A Smith, Eva Maria Novoa bioRxiv 525741; doi: https://doi.org/x.1101/525741
"Dart-seq: an antibiotic-free method for global m6A detection" Nature Methods https://doi.org/10.1038/s41592-019-0570-0
"Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates" The Eukaryotic RNA Exosome. Nov 2019. https://doi.org/10.1007/978-ane-4939-9822-7_10
"Evolutionary forces on A-to-I RNA editing revealed past sequencing individual honeybee drones". Yuange Duan, Shengqian Dou, Jiaxing Huang, Eli Eisenberg, Jian Lu . 2020 . https://doi.org/10.1101/2020.01.15.907287
"Sci-fate characterizes the dynamics of gene expression in unmarried cells" (2020) Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0480-9
"Mutations in virus-derived small-scale RNAs" Nigam Deepti; LaTourrette, Katherine; Garcia-Ruiz, Hernan. Scientific Reports (Nature Publisher Grouping); London Vol. ten, Iss. 1, (2020). DOI:x.1038/s41598-020-66374-2
Qiu, Q., Hu, P., Qiu, X. et al. Massively parallel and fourth dimension-resolved RNA sequencing in single cells with scNT-seq. Nat Methods (2020). https://doi.org/10.1038/s41592-020-0935-4
FUJIKURA, 1000. et al. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut, [due south. fifty.], 2020. DOI x.1136/gutjnl-2020-321217
Gao, Y., Liu, 10., Wu, B. et al. Quantitative profiling of N6-methyladenosine at single-base resolution in stalk-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol 22, 22 (2021). https://doi.org/10.1186/s13059-020-02241-vii
Liu H., Begik O., Novoa Due east.M. (2021) EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing. In: McMahon M. (eds) RNA Modifications. Methods in Molecular Biology, vol 2298. Humana, New York, NY. https://doi.org/x.1007/978-1-0716-1374-0_3
Yang & al. "Sequencing 5-Formyluracil in Genomic DNA at Single-Base Resolution" (2021) Analytical Chemistry doi: 10.1021/acs.analchem.1c03339

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Source: http://lindenb.github.io/jvarkit/Sam2Tsv.html