Biostar9566948

Last commit

Trim Reads So Only First Base Remains

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar biostar9566948  [options] Files

Usage: biostar9566948 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --disable-soft-clipping, -S
      disable soft clipping. Remove bases.
      Default: false
    -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/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]
    --validation-stringency
      SAM Reader Validation Stringency
      Default: LENIENT
      Possible Values: [STRICT, LENIENT, SILENT]
    --version
      print version and exit

Keywords

bam
sam

Creation Date

20230621

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar9566948.java

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 biostar9566948 ? 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/jvarkit.jar biostar9566948 -R src/test/resources/rotavirus_rf.fa src/test/resources/S1.bam   -S 
@HD VN:1.6  SO:coordinate
@SQ SN:RF01 LN:3302
@SQ SN:RF02 LN:2687
@SQ SN:RF03 LN:2592
@SQ SN:RF04 LN:2362
@SQ SN:RF05 LN:1579
@SQ SN:RF06 LN:1356
@SQ SN:RF07 LN:1074
@SQ SN:RF08 LN:1059
@SQ SN:RF09 LN:1062
@SQ SN:RF10 LN:751
@SQ SN:RF11 LN:666
@RG ID:S1   SM:S1   LB:L1   CN:Nantes
@CO biostar9566948. compilation:20230621100700 githash:8a9a881b htsjdk:3.0.4 date:20230621100755. cmd:-R src/test/resources/rotavirus_rf.fa src/test/resources/S1.bam -S
RF01_1_483_2:0:0_3:0:0_41   163 RF01    1   60  1=  =   414 483 G   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:60 XS:i:0
RF01_8_542_1:0:0_2:0:0_95   99  RF01    8   60  1=  =   473 535 A   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:69 XS:i:0
RF01_11_507_0:0:0_1:0:0_9e  99  RF01    11  60  1=  =   438 497 G   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:70 XS:i:0
RF01_12_501_0:0:0_2:0:0_62  99  RF01    12  60  1=  =   432 490 C   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:70 XS:i:0
RF01_27_590_3:0:0_1:0:0_68  163 RF01    27  60  1=  =   521 564 G   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:55 XS:i:0
RF01_44_622_1:0:0_1:0:0_3a  99  RF01    44  60  1=  =   553 579 C   2   MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:65 XS:i:0

$ java -jar dist/jvarkit.jar biostar9566948 -R src/test/resources/rotavirus_rf.fa src/test/resources/S1.bam 
@HD VN:1.6  SO:coordinate
@SQ SN:RF01 LN:3302
@SQ SN:RF02 LN:2687
@SQ SN:RF03 LN:2592
@SQ SN:RF04 LN:2362
@SQ SN:RF05 LN:1579
@SQ SN:RF06 LN:1356
@SQ SN:RF07 LN:1074
@SQ SN:RF08 LN:1059
@SQ SN:RF09 LN:1062
@SQ SN:RF10 LN:751
@SQ SN:RF11 LN:666
@RG ID:S1   SM:S1   LB:L1   CN:Nantes
@CO biostar9566948. compilation:20230621100700 githash:8a9a881b htsjdk:3.0.4 date:20230621100859. cmd:-R src/test/resources/rotavirus_rf.fa src/test/resources/S1.bam
RF01_1_483_2:0:0_3:0:0_41   163 RF01    1   60  1=69S   =   414 483 GGCTATTAAAGCTATACAATGGGGCCGTATAATCTAATCTTGTCAGAATATTTATCATTTATATATAACT  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:60 XS:i:0
RF01_8_542_1:0:0_2:0:0_95   99  RF01    8   60  1=69S   =   473 535 AAAGCTATACAATGGGGAAGTATAATCTAATCTTGTCAGAATATTTATCATTTATATATAACTCACAATG  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:69 XS:i:0
RF01_11_507_0:0:0_1:0:0_9e  99  RF01    11  60  1=69S   =   438 497 GCTATACAATGGGGAAGTATAATCTAATCTTGTCAGAATATTTATCATTTATATATAACTCACAATCCGC  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:70 XS:i:0
RF01_12_501_0:0:0_2:0:0_62  99  RF01    12  60  1=69S   =   432 490 CTATACAATGGGGAAGTATAATCTAATCTTGTCAGAATATTTATCATTTATATATAACTCACAATCCGCA  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:70 XS:i:0
RF01_27_590_3:0:0_1:0:0_68  163 RF01    27  60  1=69S   =   521 564 GTATCATCTAATCTTGTCATAATATTTATCATATATATATAACTCACAATCCGCAGTTCAAATTCCAATA  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:55 XS:i:0
RF01_44_622_1:0:0_1:0:0_3a  99  RF01    44  60  1=69S   =   553 579 CAGAATATTTATCATTTATATATAACTCAGAATCCGCAGTTCAAATTCCAATATACTATTCTTCCAATAG  2222222222222222222222222222222222222222222222222222222222222222222222  MC:Z:M1 RG:Z:S1 NM:i:0  AS:i:65 XS:i:0