jvarkit
PrettySam
Pretty SAM alignments
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar prettysam [options] Files
Usage: prettysam [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
-cN, --collapse-N
collapse cigar operator 'N'
Default: false
-cD, --collapse-ND
collapse cigar operator 'D'
Default: false
-color, --colors
using ansi escape colors
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-kg, --knowngenes
Transcrips as genpred format
https://genome.ucsc.edu/FAQ/FAQformat.html#format9 . The genePred
format is a compact alternative to GFF/GTF because one transcript is
described using only one line. Beware chromosome names are formatted the
same as your REFERENCE. A typical KnownGene file is
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz
.If you only have a gff file, you can try to generate a knownGene file
with [http://lindenb.github.io/jvarkit/Gff2KnownGene.html](http://lindenb.github.io/jvarkit/Gff2KnownGene.html)
Memory intensive: the file is loaded in memory.
-nA, --no-alignment
hide alignment
Default: false
-nT, --no-attributes
hide attributes table
Default: false
-nC, --no-cigar
hide cigar string
Default: false
-noclip, --noclip, --no-clipping
hide clipped bases
Default: false
-nP, --no-program-record
hide program record
Default: false
-nR, --no-read-group
hide read group
Default: false
-nS, --no-suppl
hide supplementary alignements
Default: false
--no-unicode
disable unicode to display ascii histogram
Default: false
-o, --out
Output file. Optional . Default: stdout
-R, --reference
Indexed fasta Reference file. This file must be indexed with samtools
faidx and with picard/gatk CreateSequenceDictionary or samtools dict
--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;,]'
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--trim
trim long string to this length. <1 = do not trim.
Default: 50
-u, --unstranslated
[20171219]Show untranslated regions (used with option -kg)
Default: false
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
-V, --variant, --vcf
[20171220]Show VCF data. VCf must be indexed. if VCF has no genotype,
the variant positions are shown, otherwise, the genotypes associated to
the read will be show.
--version
print version and exit
Keywords
- sam
- bam
Creation Date
20171215
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 prettysam ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
- PrettySam : a SAM/BAM prettifier. Lindenbaum & al. 2018. figshare. https://doi.org/10.6084/m9.figshare.5853798.v1
About long reads
The htsjdk currently (2012-12-16) doesn’t support more than 65635 cigar operations.
Example
$ java -jar dist/prettysam.jar -R ref.fa S1.bam
>>>>> 1
Read-Name : rotavirus_1_317_5:0:0_7:0:0_2de
Flag : 99
read paired : 1
proper pair : 2
mate reverse strand : 32
first of pair : 64
MAPQ : 60
Contig : rotavirus (index:0)
Start : 1
End : 70
Strand : +
Insert-Size : 317
Mate-Contig : rotavirus (index:0)
Mate-Start : 248
Mate-Strand : -
Read Group :
ID : S1
SM : S1
Read-Length : 70
Cigar : 70M (N=1)
Sequence :
Read (0) : GGCTTTTAAT GCTTTTCAGT GGTTGCTGCT CAATATGGCG TCAACTCAGC AGATGGTCAG
Mid : |||||||||| |||||||||| |||||||||| ||| |||| | || ||||||| ||||||| ||
Ref (1) : GGCTTTTAAT GCTTTTCAGT GGTTGCTGCT CAAGATGGAG TCTACTCAGC AGATGGTAAG
Op : MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM
Qual : ++++++++++ ++++++++++ ++++++++++ ++++++++++ ++++++++++ ++++++++++
Ref-Pos : 1 11 21 31 41 51
Read (60) : CTCTAATATT
Mid : ||||| ||||
Ref (61) : CTCTATTATT
Op : MMMMMMMMMM
Qual : ++++++++++
Ref-Pos : 61
Tags :
MD : 33G4A3T14A7T4 "String for mismatching positions"
NM : 5 "Edit distance to the reference"
AS : 45 "Alignment score generated by aligner"
XS : 0 "Reserved for end users"
<<<<< 1
>>>>> 2
Read-Name : rotavirus_1_535_4:0:0_4:0:0_1a6
Flag : 163
read paired : 1
proper pair : 2
mate reverse strand : 32
second of pair : 128
MAPQ : 60
Contig : rotavirus (index:0)
Start : 1
End : 70
Strand : +
Insert-Size : 535
Mate-Contig : rotavirus (index:0)
Mate-Start : 466
Mate-Strand : -
Read Group :
ID : S1
SM : S1
Read-Length : 70
Cigar : 70M (N=1)
Sequence :
Read (0) : GGCTTTTACT GCTTTTCAGT GGTTGCTTCT CAAGATGGAG TGTACTCATC AGATGGTAAG
Mid : |||||||| | |||||||||| ||||||| || |||||||||| | |||||| | ||||||||||
Ref (1) : GGCTTTTAAT GCTTTTCAGT GGTTGCTGCT CAAGATGGAG TCTACTCAGC AGATGGTAAG
Op : MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM
Qual : ++++++++++ ++++++++++ ++++++++++ ++++++++++ ++++++++++ ++++++++++
Ref-Pos : 1 11 21 31 41 51
Read (60) : CTCTATTATT
Mid : ||||||||||
Ref (61) : CTCTATTATT
Op : MMMMMMMMMM
Qual : ++++++++++
Ref-Pos : 61
Tags :
MD : 8A18G13C6G21 "String for mismatching positions"
NM : 4 "Edit distance to the reference"
AS : 50 "Alignment score generated by aligner"
XS : 0 "Reserved for end users"
<<<<< 2
Displaying genes:
$ wget -O knownGene.txt.gz "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz"
$ wget -O - "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam" |\
java -jar dist/prettysam.jar -R "http://genome.cse.ucsc.edu/cgi-bin/das/hg19/" -kg knownGene.txt.gz
(...)
>>>>> 724
Read-Name : SOLEXA-1GA-2_2_FC20EMB:5:4:549:957
Flag : 0
MAPQ : 25
Contig : chr1 (index:0)
Start : 1,115,507
End : 1,115,542
Strand : -->
Read-Length : 36
Cigar : 36M (N=1)
Sequence :
Read (0) : GGCCGGACCT GGAGGGGGCA GAAAGAGCCT CCGCAA
Middle : |||||||||| |||||||||| |||||||||| | || |
Ref (1,115,507) : ggccggacct ggagggggca gaaagagcct ctgcca
Cigar-Operator : MMMMMMMMMM MMMMMMMMMM MMMMMMMMMM MMMMMM
Qual : TRGI^WDHH` RHIMOILGEF G@C>D>GC@= D@=A>@
Ref-Pos : 1115507 1115517 1115527 1115537
uc001acy.2(+) type : EEEEEEEEEE EEEEEEEEEE EEEEEEEEEE EEEEEE
cDNA-Pos : 293 303 313 323
Pep-Pos : 98 101 105 108
Amino-Acid : lyProAspLe uGluGlyAla GluArgAlaS erAlaT
uc010nyg.1(+) type : EEEEEEEEEE EEEEEEEEEE EEEEEEEEEE EEEEEE
cDNA-Pos : 293 303 313 323
Pep-Pos : 98 101 105 108
Amino-Acid : lyProAspLe uGluGlyAla GluArgAlaS erAlaT
uc001acz.2(+) type : EEEEEEEEEE EEEEEEEEEE EEEEEEEEEE EEEEEE
cDNA-Pos : 74 84 94 104
Pep-Pos : 25 28 32 35
Amino-Acid : lyProAspLe uGluGlyAla GluArgAlaS erAlaT
Tags :
X1 : 1 "Reserved for end users"
MD : 31C2A1 "String for mismatching positions"
NM : 1 "Edit distance to the reference"
<<<<< 724
Screenshots
https://twitter.com/yokofakun/status/943132603539914752
https://twitter.com/yokofakun/status/942688906620887040
https://twitter.com/yokofakun/status/941775073156968451
