jvarkit
VcfToTable
convert a vcf to a table, to ease display in the terminal
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar vcf2table [options] Files
Usage: vcf2table [options] Files
Options:
--chartsize
google charts dimension (HTML only). Format (integer)x(integer). eg:
'1000x500' or (width) e.g: '1000'
--color, --colors
[20170808] Print Terminal ANSI colors.
Default: false
--format
[20171020] output format.
Default: text
Possible Values: [text, html]
--google
use google charts (HTML only)
Default: false
-H, --header
Print Header
Default: false
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-hide, --hide
Comma separated things to hide: FILTER,ALLELE,FILTER,SPLICEAI,INFO,VEP,SNPEFF,BCSQ,SNPEFF,SMOOVE,URL,GENOTYPE,HR,NC,GTYPE,GTYPE
. HR: homozygous on ref. NC: no-call.
Default: <empty string>
-L, -limit, --limit
Limit the number of output variant. '-1' == ALL/No limit.
Default: -1
--no-html-header
[20171023] ignore html header for HTML output.
Default: false
-o, --output
Output file. Optional . Default: stdout
-p, --ped, --pedigree
Optional Pedigree file:A pedigree file. tab delimited. Columns:
family,id,father,mother,
sex:(0|.|undefined|unknown:unknown;1|male|M:male;2|female|F:female),
phenotype
(-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected)
If undefined, this tool will try to get the pedigree from the header.
--url
A custom URL for a web browser. The following words will be replaced by
their values: ${CHROM}, ${START}, ${END}. For example for IGV that would
be: 'http://localhost:60151/goto?locus=${CHROM}%3A${START}-${END}' (see
http://software.broadinstitute.org/software/igv/book/export/html/189)
--version
print version and exit
Keywords
- vcf
- table
- visualization
See also in Biostars
Creation Date
20170511
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 vcf2table ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
- Vcf2table : a VCF prettifier. Lindenbaum & al. 2018. figshare. https://doi.org/10.6084/m9.figshare.5853801
Example
$ cat input.ped
FAM M10475 0 0 1 1
FAM M10478 0 0 2 0
FAM M10500 M10475 M10478 2 1
$ curl -s "https://raw.githubusercontent.com/arq5x/gemini/master/test/test.region.vep.vcf" | java -jar dist/vcf2table.jar -H -p input.ped
INFO
+-----------------+---------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------+
| ID | Type | Count | Description |
+-----------------+---------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------+
| AC | Integer | | Allele count in genotypes, for each ALT allele, in the same order as listed |
| AF | Float | | Allele Frequency, for each ALT allele, in the same order as listed |
| AN | Integer | 1 | Total number of alleles in called genotypes |
| BaseQRankSum | Float | 1 | Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities |
| CSQ | String | | Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE|ALLELE_NUM |
| DP | Integer | 1 | Approximate read depth; some reads may have been filtered |
| DS | Flag | 0 | Were any of the samples downsampled? |
| Dels | Float | 1 | Fraction of Reads Containing Spanning Deletions |
| FS | Float | 1 | Phred-scaled p-value using Fisher's exact test to detect strand bias |
| HRun | Integer | 1 | Largest Contiguous Homopolymer Run of Variant Allele In Either Direction |
| HaplotypeScore | Float | 1 | Consistency of the site with at most two segregating haplotypes |
| InbreedingCoeff | Float | 1 | Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation |
| MQ | Float | 1 | RMS Mapping Quality |
| MQ0 | Integer | 1 | Total Mapping Quality Zero Reads |
| MQRankSum | Float | 1 | Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities |
| QD | Float | 1 | Variant Confidence/Quality by Depth |
| ReadPosRankSum | Float | 1 | Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias |
+-----------------+---------+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------+
FORMAT
+----+---------+-------+----------------------------------------------------------------------------------------+
| ID | Type | Count | Description |
+----+---------+-------+----------------------------------------------------------------------------------------+
| AD | Integer | | Allelic depths for the ref and alt alleles in the order listed |
| DP | Integer | 1 | Approximate read depth (reads with MQ=255 or with bad mates are filtered) |
| GQ | Integer | 1 | Genotype Quality |
| GT | String | 1 | Genotype |
| PL | Integer | | Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification |
+----+---------+-------+----------------------------------------------------------------------------------------+
Dict
+-----------------------+-----------+------+
| Name | Length | AS |
+-----------------------+-----------+------+
| chr1 | 249250621 | hg19 |
(...)
| chrX | 155270560 | hg19 |
| chrY | 59373566 | hg19 |
+-----------------------+-----------+------+
Samples
+--------+---------+--------+--------+--------+------------+
| Family | Sample | Father | Mother | Sex | Status |
+--------+---------+--------+--------+--------+------------+
| FAM | M10475 | | | male | affected |
| FAM | M10478 | | | female | unaffected |
| FAM | M10500 | M10475 | M10478 | female | affected |
| FAM | M128215 | M10500 | | male | unaffected |
+--------+---------+--------+--------+--------+------------+
>>chr1/10001/T (n 1)
Variant
+--------+--------------------+
| Key | Value |
+--------+--------------------+
| CHROM | chr1 |
| POS | 10001 |
| end | 10001 |
| ID | . |
| REF | T |
| ALT | TC |
| QUAL | 175.91000000000003 |
| FILTER | |
| Type | INDEL |
+--------+--------------------+
Alleles
+-----+-----+-----+-------+--------+----+----+-----+-------------+---------------+---------+-----------+
| Idx | REF | Sym | Bases | Length | AC | AN | AF | AC_affected | AC_unaffected | AC_male | AC_female |
+-----+-----+-----+-------+--------+----+----+-----+-------------+---------------+---------+-----------+
| 0 | * | | T | 1 | 4 | 8 | 0.5 | 2 | 1 | 1 | 2 |
| 1 | | | TC | 2 | 4 | 8 | 0.5 | 2 | 1 | 1 | 2 |
+-----+-----+-----+-------+--------+----+----+-----+-------------+---------------+---------+-----------+
INFO
+----------------+-------+----------+
| key | Index | Value |
+----------------+-------+----------+
| AC | | 4 |
| AF | | 0.50 |
| AN | | 8 |
| BaseQRankSum | | 4.975 |
| DP | | 76 |
| FS | | 12.516 |
| HRun | | 0 |
| HaplotypeScore | | 218.6157 |
| MQ | | 35.31 |
| MQ0 | | 0 |
| MQRankSum | | -0.238 |
| QD | | 2.31 |
| ReadPosRankSum | | 2.910 |
+----------------+-------+----------+
VEP
+--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
| PolyPhen | EXON | SIFT | ALLELE_NUM | Gene | SYMBOL | Protein_position | Consequence | Amino_acids | Codons | Feature | BIOTYPE |
+--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
| probably_damaging(0.956) | 8/9 | deleterious(0) | 1 | ENSG00000102967 | DHODH | 346/395 | missense_variant | R/W | Cgg/Tgg | ENST00000219240 | protein_coding |
| | 3/4 | | 1 | ENSG00000102967 | DHODH | | non_coding_exon_variant&nc_transcript_variant | | | ENST00000571392 | retained_intron |
| | | | 1 | ENSG00000102967 | DHODH | | downstream_gene_variant | | | ENST00000572003 | retained_intron |
| | | | 1 | ENSG00000102967 | DHODH | | downstream_gene_variant | | | ENST00000573843 | retained_intron |
| | | | 1 | ENSG00000102967 | DHODH | | downstream_gene_variant | | | ENST00000573922 | processed_transcript |
| | | | 1 | ENSG00000102967 | DHODH | -/193 | intron_variant | | | ENST00000574309 | protein_coding |
| probably_damaging(0.946) | 8/9 | deleterious(0) | 1 | ENSG00000102967 | DHODH | 344/393 | missense_variant | R/W | Cgg/Tgg | ENST00000572887 | protein_coding |
+--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
Genotypes
+---------+------+-------+----+----+-----+---------+
| Sample | Type | AD | DP | GQ | GT | PL |
+---------+------+-------+----+----+-----+---------+
| M10475 | HET | 10,2 | 15 | 10 | 0/1 | 25,0,10 |
| M10478 | HET | 10,4 | 16 | 5 | 0/1 | 40,0,5 |
| M10500 | HET | 10,10 | 21 | 7 | 0/1 | 111,0,7 |
| M128215 | HET | 15,5 | 24 | 0 | 0/1 | 49,0,0 |
+---------+------+-------+----+----+-----+---------+
TRIOS
+-----------+-----------+-----------+-----------+----------+----------+-----------+
| Father-ID | Father-GT | Mother-ID | Mother-GT | Child-ID | Child-GT | Incompat. |
+-----------+-----------+-----------+-----------+----------+----------+-----------+
| M10475 | 0/1 | M10478 | 0/1 | M10500 | 0/1 | |
+-----------+-----------+-----------+-----------+----------+----------+-----------+
<<chr1/10001/T n 1
(...)
Html output:
$ java -jar dist/vcf2table.jar file.vcf --color --format html > out.html
Screenshots
https://twitter.com/yokofakun/status/1067730485487366145
https://twitter.com/yokofakun/status/922475502933368832
https://twitter.com/yokofakun/status/1127832269606072320
