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SAM2Tsv

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Pierre Lindenbaum edited this page Sep 8, 2015 · 13 revisions

Motivation

display a tabular view of each base of the reads vs the reference.

Compilation

See also Compilation.

$ make sam2tsv

Synopsis

$ java -jar dist/sam2tsv.jar [options] -r ref.fa (stdin |file1.sam.. fileX.bam) > out.txt

Options

Option Description
-r (fasta) The reference sequence as a FASTA file and indexed with samtools faidx + picard CreateSequenceDictionary
-A print Alignments
-h get help (this screen) and exit.
-v print version and exit.
-L (level) log level. One of java.util.logging.Level . Optional.
--doap prints a XML description of the program and exit

Output

Columns are:

  • read name
  • read flags
  • reference name
  • read-pos
  • read-base
  • read-qual
  • ref-pos
  • ref-base
  • cigar-op

Example

$ java -jar dist/sam2tsv.jar -A  \
    -r samtools-0.1.18/examples/toy.fa 
      samtools-0.1.18/examples/toy.sam
r001	163	ref	0	T	.	7	T	M
r001	163	ref	1	T	.	8	T	M
r001	163	ref	2	A	.	9	A	M
r001	163	ref	3	G	.	10	G	M
r001	163	ref	4	A	.	11	A	M
r001	163	ref	5	T	.	12	T	M
r001	163	ref	6	A	.	13	A	M
r001	163	ref	7	A	.	14	A	M
r001	163	ref	8	A	.	.	.	I
r001	163	ref	9	G	.	.	.	I
r001	163	ref	10	A	.	.	.	I
r001	163	ref	11	G	.	.	.	I
r001	163	ref	12	G	.	15	G	M
r001	163	ref	13	A	.	16	A	M
r001	163	ref	14	T	.	17	T	M
r001	163	ref	15	A	.	18	A	M
r001	163	ref	.	.	.	19	G	D
r001	163	ref	16	C	.	20	C	M
r001	163	ref	17	T	.	21	T	M
r001	163	ref	18	G	.	22	G	M
:   ref        7 TTAGATAAAGAGGATA-CTG 22      
:                ||||||||    |||| |||
:  r001        1 TTAGATAA----GATAGCTG 19      
r002	0	ref	1	A	.	.	.	I
r002	0	ref	2	A	.	.	.	I
r002	0	ref	3	A	.	9	A	M
r002	0	ref	4	G	.	10	G	M
r002	0	ref	5	A	.	11	A	M
r002	0	ref	6	T	.	12	T	M
r002	0	ref	7	A	.	13	A	M
r002	0	ref	8	A	.	14	A	M
r002	0	ref	9	G	.	.	.	I
r002	0	ref	10	G	.	.	.	I
r002	0	ref	11	G	.	15	G	M
r002	0	ref	12	A	.	16	A	M
r002	0	ref	13	T	.	17	T	M
r002	0	ref	14	A	.	18	A	M
r002	0	ref	15	A	.	.	.	I
r002	0	ref	16	A	.	.	.	I
:   ref        8 AAAGATAAGGGATAAA 18      
:                  ||||||  ||||  
:  r002        1 --AGATAA--GATA-- 17      
r003	0	ref	0	A	.	9	A	M
r003	0	ref	1	G	.	10	G	M
r003	0	ref	2	C	.	11	A	M
r003	0	ref	3	T	.	12	T	M
r003	0	ref	4	A	.	13	A	M
r003	0	ref	5	A	.	14	A	M
:   ref        4 AGCTAA 14      
:                || |||
:  r003        1 AGATAA 6       
r004	0	ref	0	A	.	16	A	M
r004	0	ref	1	T	.	17	T	M
r004	0	ref	2	A	.	18	A	M
r004	0	ref	3	G	.	19	G	M
r004	0	ref	4	C	.	20	C	M
r004	0	ref	5	T	.	21	T	M
r004	0	ref	.	.	.	22	G	N
r004	0	ref	.	.	.	23	T	N
r004	0	ref	.	.	.	24	G	N
r004	0	ref	.	.	.	25	C	N
r004	0	ref	.	.	.	26	T	N
r004	0	ref	.	.	.	27	A	N
r004	0	ref	.	.	.	28	G	N
r004	0	ref	.	.	.	29	T	N
r004	0	ref	.	.	.	30	A	N
r004	0	ref	.	.	.	31	G	N
r004	0	ref	.	.	.	32	G	N
r004	0	ref	.	.	.	33	C	N
r004	0	ref	.	.	.	34	A	N
r004	0	ref	.	.	.	35	G	N
r004	0	ref	6	C	.	.	.	I
r004	0	ref	7	T	.	36	T	M
r004	0	ref	8	C	.	37	C	M
r004	0	ref	9	A	.	38	A	M
r004	0	ref	10	G	.	39	G	M
r004	0	ref	11	C	.	40	C	M
:   ref       16 ATAGCT--------------CTCAGC 40      
:                ||||||               |||||
:  r004        1 ATAGCTGTGCTAGTAGGCAG-TCAGC 12      
r003	16	ref	0	T	.	29	T	M
r003	16	ref	1	A	.	30	A	M
r003	16	ref	2	G	.	31	G	M
r003	16	ref	3	G	.	32	G	M
r003	16	ref	4	C	.	33	C	M
:   ref       23 TAGGC 33      
:                |||||
:  r003        1 TAGGC 5       
r001	83	ref	0	C	.	37	C	M
r001	83	ref	1	A	.	38	A	M
r001	83	ref	2	G	.	39	G	M
r001	83	ref	3	C	.	40	C	M
r001	83	ref	4	G	.	41	G	M
r001	83	ref	5	C	.	42	C	M
r001	83	ref	6	C	.	43	C	M
r001	83	ref	7	A	.	44	A	M
r001	83	ref	8	T	.	45	T	M
:   ref       37 CAGCGCCAT 45      
:                |||||||||
:  r001        1 CAGCGCCAT 9       
x1	0	ref2	0	A	30	1	a	M
x1	0	ref2	1	G	30	2	g	M
x1	0	ref2	2	G	30	3	g	M
x1	0	ref2	3	T	30	4	t	M
x1	0	ref2	4	T	30	5	t	M
x1	0	ref2	5	T	30	6	t	M
x1	0	ref2	6	T	30	7	t	M
x1	0	ref2	7	A	30	8	a	M
x1	0	ref2	8	T	30	9	t	M
x1	0	ref2	9	A	30	10	a	M
x1	0	ref2	10	A	30	11	a	M
x1	0	ref2	11	A	30	12	a	M
x1	0	ref2	12	A	30	13	a	M
x1	0	ref2	13	C	30	14	c	M
x1	0	ref2	14	A	30	15	a	M
x1	0	ref2	15	A	30	16	a	M
x1	0	ref2	16	A	30	17	t	M
x1	0	ref2	17	T	30	18	t	M
x1	0	ref2	18	A	30	19	a	M
x1	0	ref2	19	A	30	20	a	M
:  ref2        1 AGGTTTTATAAAACAAATAA 20      
:                |||||||||||||||| |||
:    x1        1 aggttttataaaacaattaa 20      
x2	0	ref2	0	G	30	2	g	M
x2	0	ref2	1	G	30	3	g	M
x2	0	ref2	2	T	30	4	t	M
x2	0	ref2	3	T	30	5	t	M
x2	0	ref2	4	T	30	6	t	M
x2	0	ref2	5	T	30	7	t	M
x2	0	ref2	6	A	30	8	a	M
x2	0	ref2	7	T	30	9	t	M
x2	0	ref2	8	A	30	10	a	M
x2	0	ref2	9	A	30	11	a	M
x2	0	ref2	10	A	30	12	a	M
x2	0	ref2	11	A	30	13	a	M
x2	0	ref2	12	C	30	14	c	M
x2	0	ref2	13	A	30	15	a	M
x2	0	ref2	14	A	30	16	a	M
x2	0	ref2	15	A	30	17	t	M
x2	0	ref2	16	T	30	18	t	M
x2	0	ref2	17	A	30	19	a	M
x2	0	ref2	18	A	30	20	a	M
x2	0	ref2	19	T	30	21	g	M
x2	0	ref2	20	T	30	22	t	M
:  ref2        2 GGTTTTATAAAACAAATAATT 22      
:                ||||||||||||||| ||| |
:    x2        1 ggttttataaaacaattaagt 21      
(...)

Main source code

https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/sam2tsv/Sam2Tsv.java

##History

  • Moved to a standard argc/argv command line
  • 2014-04: added qual and samflag. Fixed a bug in soft-clip
  • 2014-11: manage hard+soft clip

##See also

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

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License

The project is licensed under the MIT license.

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