jvarkit
VcfMultiToOne
Convert VCF with multiple samples to a VCF with one SAMPLE, duplicating variant and adding the sample name in the INFO column. Never used.
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcfmulti2one [options] Files
Usage: vcfmulti2one [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
--disable-vc-attribute-recalc
When genotypes are removed/changed, Dd not recalculate variant
attributes like DP, AF, AC, AN...
Default: false
-r, --hr, -hr, --discard_hom_ref
discard if variant is hom-ref
Default: false
-c, --nc, -nc, --discard_no_call
discard if variant is no-call
Default: false
-a, --discard_non_available
discard if variant is not available (see htsjdk definition 'available if
the type of this genotype is set')
Default: false
--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].
--no-origin
do not include origin of variant
Default: false
-o, --output
Output file. Optional . Default: stdout
--regions
Optional. 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;,]'
--vc-attribute-recalc-ignore-filtered
When recalculating variant attributes like DP AF, AC, AN, ignore
FILTERed **Genotypes**
Default: false
--vc-attribute-recalc-ignore-missing
Ignore missing VCF headers (DP, AF, AC, AN). Default behavior: adding
VCF header if they're missing
Default: false
--version
print version and exit
Keywords
- vcf
- sample
See also in Biostars
Creation Date
20150312
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 vcfmulti2one ? 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
Deprecated
I don’t use this software anymore.
Input
if there is only one input with the ‘.list’ suffix, it is interpreted as a file containing the path to the vcf files
A file with the suffixes ‘.zip’ or ‘.tar’ or ‘.tar.gz’ is interpreted as an archive and all the entries looking like a vcf are extracted.
24 fev 2020: refactored, the input is not anymore sorted. Use bcftools sort
Example
with zip and tar
$ tar tvfz ~/jeter.tar.gz && unzip -l ~/jeter.zip && java -jar dist/jvarkit.jar vcfmulti2one ~/jeter.tar.gz ~/jeter.zip | bcftools view - | wc -l
-rw-r--r-- lindenb/lindenb 5805 2019-01-11 18:29 src/test/resources/rotavirus_rf.ann.vcf.gz
-rw-r--r-- lindenb/lindenb 27450 2019-01-11 18:29 src/test/resources/rotavirus_rf.freebayes.vcf.gz
-rw-r--r-- lindenb/lindenb 7366 2019-01-11 18:29 src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz
Archive: /home/lindenb/jeter.zip
Length Date Time Name
--------- ---------- ----- ----
7366 2019-01-11 18:29 src/test/resources/rotavirus_rf.unifiedgenotyper.vcf.gz
5805 2019-01-11 18:29 src/test/resources/rotavirus_rf.ann.vcf.gz
3661 2019-01-11 18:29 src/test/resources/rotavirus_rf.vcf.gz
27450 2019-01-11 18:29 src/test/resources/rotavirus_rf.freebayes.vcf.gz
--------- -------
44282 4 files
4883
$ curl -s "http://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.genotypes.vcf.gz" |\
gunzip -c |\
java -jar dist/jvarkit.jar vcfmulti2one -c -r -a |\
grep -v '##' |\
grep -E '(CHROM|SAMPLENAME)' | head | verticalize
>>> 2
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00096;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 2
>>> 3
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00097;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 0|1
<<< 3
>>> 4
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00099;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 0|1
<<< 4
>>> 5
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .import java.util.Comparator;
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00100;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 5
>>> 6
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00102;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 6
>>> 7
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00103;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 7
>>> 8
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00105;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 8
>>> 9
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00106;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 1|0
<<< 9
>>> 10
$1 #CHROM : 1
$2 POS : 10177
$3 ID : .
$4 REF : A
$5 ALT : AC
$6 QUAL : 100
$7 FILTER : PASS
$8 INFO : AA=|||unknown(NO_COVERAGE);AC=2130;AF=0.425319;AFR_AF=0.4909;AMR_AF=0.3602;AN=5008;DP=103152;EAS_AF=0.3363;EUR_AF=0.4056;NS=2504;SAMPLENAME=HG00114;SAS_AF=0
.4949
$9 FORMAT : GT
$10 SAMPLE : 0|1
<<< 10