jvarkit
SamScanSplitReads
scan split reads
Usage
Usage: samscansplitreads [options] Files
Options:
--bcf-output
If this program writes a VCF to a file, The format is first guessed from
the file suffix. Otherwise, force BCF output. The current supported BCF
version is : 2.1 which is not compatible with bcftools/htslib (last
checked 2019-11-15)
Default: false
--buffer-size
dump buffer every 'x' bases. Most users should not use this.
Default: 10000
-x, --extend
extends interval by 'x' pb before merging.
Default: 10
--generate-vcf-md5
Generate MD5 checksum for VCF output.
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
-partition, --partition
Data partitioning using the SAM Read Group (see
https://gatkforums.broadinstitute.org/gatk/discussion/6472/ ) . It can
be any combination of sample, library....
Default: sample
Possible Values: [readgroup, sample, library, platform, center, sample_by_platform, sample_by_center, sample_by_platform_by_center, any]
-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;,]'
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
--version
print version and exit
Keywords
- sam
- sv
- splitreads
- clip
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 samscansplitreads
The java jar file will be installed in the dist directory.
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 samscansplitreads ? 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
Motivation
finds the regions having some clipped reads.
input is a set of BAM files. One file ending with ‘.list’ is interpreted as a file containing some path to the bams.
output is a VCF file
Example:
$ java -jar dist/samscansplitreads.jar src/test/resources/S*.bam 2> /dev/null
##fileformat=VCFv4.2
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=M3,Number=1,Type=Float,Description="Median size of the clip in 3'">
##FORMAT=<ID=M5,Number=1,Type=Float,Description="Median size of the clip in 5'">
##FORMAT=<ID=N3,Number=1,Type=Integer,Description="Number of clipped reads in 3'">
##FORMAT=<ID=N5,Number=1,Type=Integer,Description="Number of clipped reads in 5'">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="SV length">
##contig=<ID=RF01,length=3302>
##contig=<ID=RF02,length=2687>
##contig=<ID=RF03,length=2592>
##contig=<ID=RF04,length=2362>
##contig=<ID=RF05,length=1579>
##contig=<ID=RF06,length=1356>
##contig=<ID=RF07,length=1074>
##contig=<ID=RF08,length=1059>
##contig=<ID=RF09,length=1062>
##contig=<ID=RF10,length=751>
##contig=<ID=RF11,length=666>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S3 S4 S5 S1 S2
RF01 195 . N <SPLIT> . . DP=1;END=199;SVLEN=5 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:4.00:0:1 ./. ./.
RF01 509 . N <SPLIT> . . DP=1;END=577;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:68.00:0:1:0 ./.
RF01 725 . N <SPLIT> . . DP=2;END=793;SVLEN=69 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 ./. ./. ./. 0/1:1:68.00:0:1:0
RF01 903 . N <SPLIT> . . DP=2;END=1000;SVLEN=98 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:2:68.00:0:2:0 ./. ./.
RF01 1607 . N <SPLIT> . . DP=2;END=1616;SVLEN=10 GT:DP:M3:M5:N3:N5 0/1:1:0:9.00:0:1 ./. ./. ./. 0/1:1:0:9.00:0:1
RF01 1672 . N <SPLIT> . . DP=2;END=1682;SVLEN=11 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:9.00:0:1 ./. 0/1:1:0:3.00:0:1 ./.
RF01 1822 . N <SPLIT> . . DP=1;END=1890;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:68.00:0:1:0 ./.
RF01 1926 . N <SPLIT> . . DP=1;END=1994;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:68.00:0:1:0 ./.
RF01 2377 . N <SPLIT> . . DP=2;END=2385;SVLEN=9 GT:DP:M3:M5:N3:N5 0/1:1:0:8.00:0:1 ./. ./. ./. 0/1:1:0:8.00:0:1
RF01 2542 . N <SPLIT> . . DP=2;END=2610;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:2:68.00:4.00:1:1 ./. ./.
RF01 2689 . N <SPLIT> . . DP=1;END=2691;SVLEN=3 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:2.00:0:1 ./. ./. ./.
RF01 2719 . N <SPLIT> . . DP=2;END=2787;SVLEN=69 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 ./. ./. ./. 0/1:1:68.00:0:1:0
RF01 3230 . N <SPLIT> . . DP=2;END=3231;SVLEN=2 GT:DP:M3:M5:N3:N5 0/1:1:0:1.00:0:1 ./. ./. ./. 0/1:1:0:1.00:0:1
RF02 3 . N <SPLIT> . . DP=2;END=6;SVLEN=4 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. ./. 0/1:1:0:3.00:0:1
RF02 343 . N <SPLIT> . . DP=4;END=451;SVLEN=109 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. 0/1:2:68.00:0:2:0 0/1:1:0:3.00:0:1
RF02 513 . N <SPLIT> . . DP=1;END=581;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF02 661 . N <SPLIT> . . DP=1;END=729;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF02 818 . N <SPLIT> . . DP=4;END=848;SVLEN=31 GT:DP:M3:M5:N3:N5 0/1:2:0:8.00:0:2 ./. ./. ./. 0/1:2:0:8.00:0:2
RF02 957 . N <SPLIT> . . DP=1;END=966;SVLEN=10 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:9.00:0:1 ./. ./. ./.
RF02 1095 . N <SPLIT> . . DP=1;END=1163;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF02 1707 . N <SPLIT> . . DP=2;END=1725;SVLEN=19 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:9.00:0:1 0/1:1:0:2.00:0:1 ./. ./.
RF02 1811 . N <SPLIT> . . DP=1;END=1821;SVLEN=11 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:0:10.00:0:1 ./.
RF02 1883 . N <SPLIT> . . DP=2;END=1951;SVLEN=69 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 ./. ./. ./. 0/1:1:68.00:0:1:0
RF02 2220 . N <SPLIT> . . DP=1;END=2224;SVLEN=5 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:0:4.00:0:1 ./.
RF02 2515 . N <SPLIT> . . DP=3;END=2663;SVLEN=149 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:3:68.00:4.00:2:1 ./. ./.
RF03 500 . N <SPLIT> . . DP=2;END=569;SVLEN=70 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 0/1:1:0:2.00:0:1 ./. ./.
RF03 739 . N <SPLIT> . . DP=2;END=823;SVLEN=85 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:2:68.00:2.00:1:1 ./.
RF03 1072 . N <SPLIT> . . DP=3;END=1147;SVLEN=76 GT:DP:M3:M5:N3:N5 0/1:1:0:2.00:0:1 ./. 0/1:1:68.00:0:1:0 ./. 0/1:1:0:2.00:0:1
RF03 1207 . N <SPLIT> . . DP=3;END=1350;SVLEN=144 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:2:68.00:0:2:0 0/1:1:68.00:0:1:0 ./.
RF03 1729 . N <SPLIT> . . DP=3;END=1809;SVLEN=81 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 0/1:1:0:7.00:0:1 ./. ./. 0/1:1:68.00:0:1:0
RF03 1924 . N <SPLIT> . . DP=2;END=1926;SVLEN=3 GT:DP:M3:M5:N3:N5 0/1:1:0:2.00:0:1 ./. ./. ./. 0/1:1:0:2.00:0:1
RF03 2153 . N <SPLIT> . . DP=1;END=2221;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:68.00:0:1:0 ./. ./.
RF04 173 . N <SPLIT> . . DP=1;END=181;SVLEN=9 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:8.00:0:1 ./. ./. ./.
RF04 579 . N <SPLIT> . . DP=2;END=678;SVLEN=100 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:2:68.00:0:2:0 ./. ./.
RF04 704 . N <SPLIT> . . DP=2;END=707;SVLEN=4 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. ./. 0/1:1:0:3.00:0:1
RF04 754 . N <SPLIT> . . DP=1;END=822;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:68.00:0:1:0 ./. ./.
RF04 879 . N <SPLIT> . . DP=1;END=887;SVLEN=9 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:0:8.00:0:1 ./.
RF04 966 . N <SPLIT> . . DP=2;END=1091;SVLEN=126 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. 0/1:1:68.00:0:1:0 ./.
RF04 1119 . N <SPLIT> . . DP=1;END=1187;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF04 1378 . N <SPLIT> . . DP=1;END=1380;SVLEN=3 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:2.00:0:1 ./. ./.
RF04 1793 . N <SPLIT> . . DP=2;END=1920;SVLEN=128 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:2:68.00:0:2:0 ./.
RF04 2070 . N <SPLIT> . . DP=1;END=2071;SVLEN=2 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:0:1.00:0:1 ./.
RF05 112 . N <SPLIT> . . DP=2;END=115;SVLEN=4 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. ./. 0/1:1:0:3.00:0:1
RF05 252 . N <SPLIT> . . DP=1;END=256;SVLEN=5 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:0:4.00:0:1 ./.
RF05 427 . N <SPLIT> . . DP=1;END=433;SVLEN=7 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:6.00:0:1 ./. ./.
RF05 529 . N <SPLIT> . . DP=1;END=530;SVLEN=2 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:1.00:0:1 ./. ./.
RF05 560 . N <SPLIT> . . DP=2;END=563;SVLEN=4 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. ./. 0/1:1:0:3.00:0:1
RF05 750 . N <SPLIT> . . DP=1;END=754;SVLEN=5 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:4.00:0:1 ./. ./. ./.
RF05 841 . N <SPLIT> . . DP=1;END=909;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF05 960 . N <SPLIT> . . DP=1;END=1028;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. ./. 0/1:1:68.00:0:1:0 ./.
RF05 1434 . N <SPLIT> . . DP=1;END=1436;SVLEN=3 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:2.00:0:1 ./. ./. ./.
RF06 26 . N <SPLIT> . . DP=1;END=29;SVLEN=4 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:3.00:0:1 ./. ./.
RF06 253 . N <SPLIT> . . DP=1;END=321;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF06 465 . N <SPLIT> . . DP=2;END=533;SVLEN=69 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 ./. ./. ./. 0/1:1:68.00:0:1:0
RF06 691 . N <SPLIT> . . DP=2;END=762;SVLEN=72 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:4.00:0:1 ./. 0/1:1:68.00:0:1:0 ./.
RF06 1045 . N <SPLIT> . . DP=3;END=1133;SVLEN=89 GT:DP:M3:M5:N3:N5 ./. 0/1:2:68.00:3.00:1:1 ./. 0/1:1:68.00:0:1:0 ./.
RF06 1224 . N <SPLIT> . . DP=1;END=1292;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:68.00:0:1:0 ./. ./.
RF07 223 . N <SPLIT> . . DP=2;END=225;SVLEN=3 GT:DP:M3:M5:N3:N5 0/1:1:0:2.00:0:1 ./. ./. ./. 0/1:1:0:2.00:0:1
RF07 345 . N <SPLIT> . . DP=2;END=420;SVLEN=76 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. 0/1:1:0:4.00:0:1 ./.
RF07 790 . N <SPLIT> . . DP=1;END=792;SVLEN=3 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:2.00:0:1 ./. ./.
RF07 845 . N <SPLIT> . . DP=2;END=913;SVLEN=69 GT:DP:M3:M5:N3:N5 0/1:1:68.00:0:1:0 ./. ./. ./. 0/1:1:68.00:0:1:0
RF08 54 . N <SPLIT> . . DP=2;END=57;SVLEN=4 GT:DP:M3:M5:N3:N5 0/1:1:0:3.00:0:1 ./. ./. ./. 0/1:1:0:3.00:0:1
RF08 295 . N <SPLIT> . . DP=1;END=296;SVLEN=2 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:0:1.00:0:1 ./. ./.
RF08 668 . N <SPLIT> . . DP=1;END=736;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. 0/1:1:68.00:0:1:0 ./. ./. ./.
RF08 896 . N <SPLIT> . . DP=1;END=904;SVLEN=9 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:8.00:0:1 ./. ./. ./.
RF10 192 . N <SPLIT> . . DP=1;END=196;SVLEN=5 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:4.00:0:1 ./. ./. ./.
RF10 433 . N <SPLIT> . . DP=1;END=501;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:68.00:0:1:0 ./. ./.
RF11 7 . N <SPLIT> . . DP=3;END=133;SVLEN=127 GT:DP:M3:M5:N3:N5 ./. 0/1:1:0:5.00:0:1 0/1:1:68.00:0:1:0 0/1:1:68.00:0:1:0 ./.
RF11 179 . N <SPLIT> . . DP=1;END=247;SVLEN=69 GT:DP:M3:M5:N3:N5 ./. ./. 0/1:1:68.00:0:1:0 ./. ./.
history
- 2018-11-14 rewritten from scratch