jvarkit
Sam2Tsv
Prints the SAM alignments as a TAB delimited file.
Usage
Usage: sam2tsv [options] Files
Options:
-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
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 following
suffixes are recognized: vcf, vcf.gz bed, bed.gz, gtf, gff, gff.gz,
gtf.gz.Otherwise it could be an empty string (no interval) or a list of
plain interval separated by '[ \t\n;,]'
-N, --skip-N
Skip 'N' operator
Default: false
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
--version
print version and exit
Keywords
- sam
- bam
- table
- cram
- tsv
See also in Biostars
- https://www.biostars.org/p/157232
- https://www.biostars.org/p/59647
- https://www.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/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sam2tsv
The java jar file will be installed in the dist directory.
Creation Date
20170712
Source code
Unit Tests
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- 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.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
Example
$ java -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 30 ref 0 T . 7 T M
r001 163 30 ref 1 T . 8 T M
r001 163 30 ref 2 A . 9 A M
r001 163 30 ref 3 G . 10 G M
r001 163 30 ref 4 A . 11 A M
r001 163 30 ref 5 T . 12 T M
r001 163 30 ref 6 A . 13 A M
r001 163 30 ref 7 A . 14 A M
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 G . . . I
r001 163 30 ref 12 G . 15 G M
r001 163 30 ref 13 A . 16 A M
r001 163 30 ref 14 T . 17 T M
r001 163 30 ref 15 A . 18 A M
r001 163 30 ref . . . 19 G D
r001 163 30 ref 16 C . 20 C M
r001 163 30 ref 17 T . 21 T M
r001 163 30 ref 18 G . 22 G M
r002 0 30 ref 0 A . 8 T S
r002 0 30 ref 1 A . . . I
r002 0 30 ref 2 A . . . I
r002 0 30 ref 3 A . 9 A M
r002 0 30 ref 4 G . 10 G M
r002 0 30 ref 5 A . 11 A M
r002 0 30 ref 6 T . 12 T M
r002 0 30 ref 7 A . 13 A M
r002 0 30 ref 8 A . 14 A M
r002 0 30 ref . . . . . P
r002 0 30 ref 9 G . . . I
r002 0 30 ref . . . . . P
r002 0 30 ref 10 G . . . I
r002 0 30 ref 11 G . 15 G M
r002 0 30 ref 12 A . 16 A M
(...)
Example 2
sam2tsv can read data from a linux pipe.
samtools view -h input.bam | java -jar dist/sam2tsv.jar
Citations
Sam2tsv was cited in :
- “Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, 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: 10.1371/journal.pone.0106689 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106689
- “High-Throughput Identification of Genetic Variation Impact 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 impact on genome evolution “ Molecular Biology and Evolution, msx274, https://doi.org/10.1093/molbev/msx274
- “Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency” Genome Biology201819:71 https://doi.org/10.1186/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/10.1101/525741
- “DART-seq: an antibody-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/10.1007/978-1-4939-9822-7_10
- “Evolutionary forces on A-to-I RNA editing revealed by 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 single cells” (2020) Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0480-9
- “Mutations in virus-derived small RNAs” Nigam Deepti; LaTourrette, Katherine; Garcia-Ruiz, Hernan. Scientific Reports (Nature Publisher Group); London Vol. 10, Iss. 1, (2020). DOI:10.1038/s41598-020-66374-2
- Qiu, Q., Hu, P., Qiu, X. et al. Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Nat Methods (2020). https://doi.org/10.1038/s41592-020-0935-4
- FUJIKURA, K. et al. Multiregion whole-exome sequencing of intraductal papillary mucinous neoplasms reveals frequent somatic KLF4 mutations predominantly in low-grade regions. Gut, [s. l.], 2020. DOI 10.1136/gutjnl-2020-321217
- Gao, Y., Liu, X., Wu, B. et al. Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol 22, 22 (2021). https://doi.org/10.1186/s13059-020-02241-7