jvarkit
SamSlop
extends sam by ‘x’ bases using the reference sequence
Usage
Usage: SamSlop [options] Files
Options:
--bamcompression
Compression Level. 0: no compression. 9: max compression;
Default: 5
-q, --defaultQual
default base quality (one letter)
Default: #
-M, --extend3
num bases to extends on 3'
Default: 0
-m, --extend5
num bases to extends on 5'
Default: 0
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --out
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;,]'
-c, --rmClip
remove clipped bases
Default: false
--samoutputformat
Sam output format.
Default: SAM
Possible Values: [BAM, SAM, CRAM]
--validation-stringency
SAM Reader Validation Stringency
Default: LENIENT
Possible Values: [STRICT, LENIENT, SILENT]
--version
print version and exit
Keywords
- sam
- bam
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 SamSlop
The java jar file will be installed in the dist directory.
Creation Date
20160119
Source code
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 SamSlop ? 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/samslop.jar -m 20 -M 10 -r ~/src/gatk-ui/testdata/ref.fa ~/src/gatk-ui/testdata/S1.bam
@HD VN:1.5 GO:none SO:unsorted
@SQ SN:rotavirus LN:1074
@RG ID:S1 SM:S1
@PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_01_R1.fq.gz S1_01_R2.fq.gz
@PG ID:bwa.1 PN:bwa VN:0.7.12-r1044 CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_02_R1.fq.gz S1_02_R2.fq.gz
@PG ID:bwa.2 PN:bwa VN:0.7.12-r1044 CL:../bwa/bwa mem -R @RG\tID:S1\tSM:S1 ref.fa S1_03_R1.fq.gz S1_03_R2.fq.gz
rotavirus_1_317_5:0:0_7:0:0_2de 99 rotavirus 1 60 140M = 248 317 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAATATGGCGTCAACTCAGCAGATGGTCAGCTCTAATATTAATACTTCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:33G4A3T14A7T4 RG:Z:S1 NM:i:5 AS:i:45 XS:i:0
rotavirus_1_535_4:0:0_4:0:0_1a6 163 rotavirus 1 60 140M = 466 535 GGCTTTTACTGCTTTTCAGTGGTTGCTTCTCAAGATGGAGTGTACTCATCAGATGGTAAGCTCTATTATTAATACTTCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:8A18G13C6G21 RG:Z:S1 NM:i:4 AS:i:50 XS:i:0
rotavirus_1_543_5:0:0_11:0:0_390 163 rotavirus 1 60 140M = 487 530 GGCTTTTAATGCTTTTCATTTGATGCTGCTCAAGATGGAGTCTACACAGCAGATGGTCAGCTCTATTATTAATACTTCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:18G1G1T22T11A12 RG:Z:S1 NM:i:5 AS:i:45 XS:i:0
rotavirus_1_578_3:0:0_7:0:0_7c 99 rotavirus 1 60 140M = 509 578 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTCCTGAGCAGCTGGTAAGCTCTATTATTAATACTTCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:43A2C5A17 RG:Z:S1 NM:i:3 AS:i:55 XS:i:0
rotavirus_1_497_4:0:0_5:0:0_2f6 163 rotavirus 1 60 140M = 432 497 GGCATTTAATGCTTAACAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTCTTATTAATACTTCTT ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:3T10T0T48A5 RG:Z:S1 NM:i:4 AS:i:51 XS:i:0
rotavirus_2_509_4:0:0_8:0:0_68 99 rotavirus 1 60 4M = 440 478 GGCTTTTAAAGCTTTTCAGTTGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGTTACGCTCTATTATTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:8T10G34G2A12 RG:Z:S1 NM:i:4 AS:i:50 XS:i:0
rotavirus_2_441_11:0:0_4:0:0_298 99 rotavirus 1 60 4M = 372 440 GGCTTTTAATGCTTTTCAGTTGTTGCTGCACAAGATGGAGTCTACACAGCAGATGGTAAGCT #+++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:19G8T15T6 RG:Z:S1 NM:i:3 AS:i:36 XS:i:0
rotavirus_2_538_5:0:0_6:0:0_6b 99 rotavirus 1 60 4M = 469 537 GGCTTTTAATGCTTTTCAGTGGTTTCTTCTCACGATGGAGTCTACTCAGCAGAAGGTAAGCACTATTATTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:23G2G4A20T7T9 RG:Z:S1 NM:i:5 AS:i:45 XS:i:0
rotavirus_2_459_8:0:0_3:0:0_388 99 rotavirus 1 60 4M = 390 458 GGCTTTTAAAGCATTACAGTTGTTGCAGCTCAAGAAGGAGACTACTCAGCAGATGGTAAGCTCTATAATTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:8T2T2T4G5T8T4T25T4 RG:Z:S1 NM:i:8 AS:i:30 XS:i:0
rotavirus_2_577_7:0:0_6:0:0_64 163 rotavirus 1 60 4M = 513 576 GGCTTTTAATTCTATTCAGTGGTTGCTGCTCCAGAAGGAGTCTACTCAGGAGATGGTACGCTCTCTTATTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:9G2T17A3T13C8A5A6 RG:Z:S1 NM:i:7 AS:i:35 XS:i:0
rotavirus_2_500_1:0:0_14:0:0_88 163 rotavirus 1 60 4M = 453 492 GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCAATTATTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:62T7 RG:Z:S1 NM:i:1 AS:i:65 XS:i:0
rotavirus_2_445_5:0:0_10:0:0_c9 163 rotavirus 1 60 4M = 377 434 GGCTTTTAATGCTTTTCAGTTGTAGCTGCTCAAGATGGAGTCTACTCATCAGATGGTAAGCTCTCTTCTTAATACTTCTTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:19G2T24G15A2A3 RG:Z:S1 NM:i:5 AS:i:48 XS:i:0
rotavirus_2_488_8:0:0_9:0:0_343 99 rotavirus 1 60 4M = 419 487 GTCTTTAAATGCTTTTCAGTGTTTGCTGCTCAAGATGGAGTCTACTCAGCAGAAGGTAAGCTCTATTATTAATA #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:0G4T14G31T10 RG:Z:S1 NM:i:4 AS:i:47 XS:i:0
rotavirus_2_478_5:0:0_5:0:0_35c 163 rotavirus 1 60 4M = 409 477 GGCATTTAATGCTTTTCAGTGGTTGCTGCACAAGATGGAGTCTACTCAGCAGATTGTAAGCTCTATTATTAATACTT #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++########## MD:Z:2T25T24G12 RG:Z:S1 NM:i:3 AS:i:53 XS:i:0
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