AlleleFrequencyCalculator

Last commit

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

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/misc/AlleleFrequencyCalculator.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/misc/AlleleFrequencyCalculatorTest.java

Contribute

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