VcfToIntervals
split a vcf to interval or bed for parallelization
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcf2intervals [options] Files
Usage: vcf2intervals [options] Files
Options:
--bed, --bed-output
force BED format as output. (Default is '.interval_list')
Default: false
-D, --distance
min size of an interval (or use option -N). A distance specified as a
positive integer.Commas are removed. The following suffixes are
interpreted : b,bp,k,kb,m,mb,g,gb
Default: -1
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
--intervals, --bed-input
Search for intervals for EACH record of the provided bed file. VCF path
must be provided and indexed.
--min-distance
extends the interval if the last variant is withing distance 'x' of the
next interval. Ignore if negative.A distance specified as a positive
integer.Commas are removed. The following suffixes are interpreted :
b,bp,k,kb,m,mb,g,gb
Default: -1
-N, --variants, --n-variants
number of variants per interval (or use option -D)
Default: -1
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
Keywords
- vcf
- bed
- interval
See also in Biostars
Creation Date
20211112
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 vcf2intervals ? 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
Input
input is a VCF file or a VCF stream. input must be sorted on chrom/pos.
Example
$ java -jar dist/vcf2intervals.jar -N 5 src/test/resources/rotavirus_rf.vcf.gz --min-distance 1
@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
@RG ID:S2 SM:S2
@RG ID:S3 SM:S3
@RG ID:S4 SM:S4
@RG ID:S5 SM:S5
@CO vcf2intervals. compilation:20211112182935 githash:9b2ab03 htsjdk:2.24.1 date:20211112183125. cmd:-N 5 src/test/resources/rotavirus_rf.vcf.gz --min-distance 1
RF01 970 970 1 1
RF02 251 1965 5 1715
RF03 1221 2150 5 930
RF03 2201 2573 3 373
RF04 887 1860 5 974
RF04 1900 1920 2 21
RF05 41 1297 5 1257
RF05 1339 1339 1 1
RF06 517 1132 5 616
RF07 98 952 4 855
RF08 926 992 2 67
RF09 294 414 3 121
RF10 46 175 3 130
RF11 74 79 1 6
$ java -jar dist/vcf2intervals.jar --distance 300 --min-distance 0 src/test/resources/rotavirus_rf.vcf.gz
@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
@RG ID:S2 SM:S2
@RG ID:S3 SM:S3
@RG ID:S4 SM:S4
@RG ID:S5 SM:S5
@CO vcf2intervals. compilation:20211112182935 githash:9b2ab03 htsjdk:2.24.1 date:20211112183310. cmd:--distance 300 --min-distance 0 src/test/resources/rotavirus_rf.vcf.gz
RF01 970 970 1 1
RF02 251 251 1 1
RF02 578 877 2 300
RF02 1726 1965 2 240
RF03 1221 1242 2 22
RF03 1688 1708 2 21
RF03 2150 2315 3 166
RF03 2573 2573 1 1
RF04 887 991 2 105
RF04 1241 1262 2 22
RF04 1857 1920 3 64
RF05 41 41 1 1
RF05 499 795 2 297
RF05 879 879 1 1
RF05 1297 1339 2 43
RF06 517 695 4 179
RF06 1129 1132 1 4
RF07 98 225 2 128
RF07 684 952 2 269
RF08 926 992 2 67
RF09 294 414 3 121
RF10 46 175 3 130
RF11 74 79 1 6