Fisher Case / Controls per Variant (Vertical)
Usage: vcfburdenrscriptv [options] Files
Options:
--cadd, -cadd
[20180831] Include CADD data, if available (INFO/CADD_PHRED
INFO/CADD_SCORE)
Default: false
-cpm, --cadd-phred-missing
[20180831] value for CADD / phred missing data
Default: NA
-csm, --cadd-score-missing
[20180921] value for CADD / score missing data
Default: NA
-f, --function
User defined R function to be called after each VCF
Default: <empty string>
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-if, --ignorefilter
accept variants having a FILTER column. Default is ignore variants with
a FILTER column
Default: false
-minusnineiszero, --minusnineiszero
No Call is '0' (default is -9)
Default: false
--nfe
[20180910] INCLUDE gnomad genome NFE AC
Default: false
-o, --output
Output file. Optional . Default: stdout
-p, --pedigree
[20180831] pedigree file (or I will try to extract the pedigree from the
vcf header. A pedigree is a text file delimited with tabs. No header.
Columns are (1) Family (2) Individual-ID (3) Father Id or '0' (4) Mother
Id or '0' (5) Sex : 1 male/2 female / 0 unknown (6) Status : 0
unaffected, 1 affected,-9 unknown
-t, --title
Try to find ##(TITLE)=abcdefghijk in the VCF header and use it as the
name of the VCF chunk
Default: <empty string>
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcfburdenrscriptv
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite vcfburdenrscriptv ? 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
Variant in that VCF should have one and only one ALT allele. Use https://github.com/lindenb/jvarkit/wiki/VcfMultiToOneAllele if needed.