VcfAncestralAllele

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Annotate a VCF with it's ancestral allele. Data from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.README

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar vcfancestralalleles  [options] Files

Usage: vcfancestralalleles [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
    --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].
  * -m, --manifest
      Manifest file containing the path to the fasta files. See doc. ALL fasta 
      files must be indexed with `samtools faidx`
    -o, --out
      Output file. Optional . Default: stdout
    -t, --tag
      Ancestral allele INFO attribute
      Default: AA
    --version
      print version and exit

Keywords

vcf
ancestral
1000k
allele

Creation Date

20180418

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/onekgenomes/VcfAncestralAllele.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/onekgenomes/VcfAncestralAlleleTest.java

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 vcfancestralalleles ? 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

Motivation

For @isamtalves : annotate a VCF for ancestral allele using data from 1000 genomes:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/human_ancestor_GRCh37_e59.README

Manifest

manifest is a tab delimited file.

empty lines are ignored

lines starting with '#' are ignored

three columns:

1st column: REF chromosome name, multiple/aliases can be separated by a pipe '|'
2nd column: ancestral contig name
3td column: File PATH to the equivalent ancestral contig.

note to self: building the manifest

 find ${PWD} -name "*.fa" | sort -V | while read F; do echo "$F" | sed 's%/commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_%%' | sed 's/.fa//' | tr -d "\n" && echo -ne "\t" &&  head -n 1 $F | cut -c 2- | tr -d '\n' && echo -en "\t" && echo $F  ; done | sed 's/^\([^\t]*\)/\1|chr\1/'

1|chr1    ANCESTOR_for_chromosome:GRCh37:1:1:249250621:1   /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_1.fa
2|chr2    ANCESTOR_for_chromosome:GRCh37:2:1:243199373:1   /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_2.fa
3|chr3    ANCESTOR_for_chromosome:GRCh37:3:1:198022430:1   /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_3.fa
4|chr4    ANCESTOR_for_chromosome:GRCh37:4:1:191154276:1   /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_4.fa
5|chr5    ANCESTOR_for_chromosome:GRCh37:5:1:180915260:1   /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/human_ancestor_5.fa

Example:

$ java -jar dist/jvarkit.jar vcfancestralalleles \
    -m /commun/data/pubdb/ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/human_ancestor_GRCh37_e59/manifest.mf \
    src/test/resources/gnomad.exomes.r2.0.1.sites.vcf.gz |\
    bcftools annotate -x '^INFO/AA'

(...)
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   905606  rs540662886 G   C,A 41743.9 PASS    AA=G
1   905608  rs770396126 G   T,A 1006.45 PASS    AA=G
1   905609  .   G   A   694.04  PASS    AA=G
1   905610  rs775689041 TG  AG,T,TGGGGGGCCCAG   4327.1  PASS    AA=TG
1   905611  rs749351425 G   T   2434.35 PASS    AA=G
1   905616  .   G   C   1801.88 PASS    AA=G
1   905617  rs376988925 C   T,G 4379.6  PASS    AA=C
1   905619  rs774441222 C   T   19350.2 PASS    AA=C
1   905621  rs368876607 G   A   14291.5 PASS    AA=G
1   905623  rs770778738 G   A   8255.09 PASS    AA=g
1   905626  .   G   A   257.48  PASS    AA=G
1   905627  rs755913930 GC  G,GCC   75797.7 PASS    AA=GC
1   905628  rs776376856 C   A   76618.4 AC0;RF  AA=C
1   905629  rs759517260 C   T   13583.4 PASS    AA=C
1   905632  .   C   T   2152.62 PASS    AA=C
1   905634  rs765105613 C   T   4534.75 PASS    AA=C
1   905635  rs752637312 C   A   4947.89 PASS    AA=C
1   905636  .   C   T   888.44  PASS    AA=C
1   905637  rs762369764 C   T   313.28  PASS    AA=C
(...)

** Cited in

"Inferences of Local Genetic Adaptation from Palaeolithic Hunter Gatherers" Dean James Cornish . Thesis. https://discovery.ucl.ac.uk/id/eprint/10170497/1/Cornish_Thesis_MPhil.pdf VcfAncestralAllele