jvarkit
AlleleFrequencyCalculator
Allele Frequency Calculator
DEPRECATED
Use bioalcidae
Usage
This program is now part of the main jvarkit tool. See jvarkit for compiling.
Usage: java -jar dist/jvarkit.jar allelefreqcalc [options] Files
Usage: allelefreqcalc [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
Keywords
- vcf
- af
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 allelefreqcalc ? 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
curl -s "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.chr22.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz" | gunzip -c | \
java -jar dist/allelefreqcalc.jar | head
CHR POS ID REF ALT TOTAL_CNT ALT_CNT FRQ
22 16050408 rs149201999 T C 2184 134 0.06135531
22 16050612 rs146752890 C G 2184 184 0.08424909
22 16050678 rs139377059 C T 2184 113 0.051739927
22 16050984 rs188945759 C G 2184 5 0.0022893774
22 16051107 rs6518357 C A 2184 127 0.058150183
22 16051249 rs62224609 T C 2184 157 0.07188645
22 16051347 rs62224610 G C 2184 650 0.29761904
22 16051453 rs143503259 A C 2184 160 0.07326008
22 16051477 rs192339082 C A 2184 2 9.157509E-4