Set ancestral alleles to upper case in vcf file

Question

[spiral01]

I am trying to set my reference allele as the ancestral allele in 1000genomes vcf files. I can do this using the --derived option in vcftools. However most of the ancestral alleles are in lowercase so vcftools is not able to correct for this.

I am currently looking at a method of extracting the ancestral alleles and converting them to upper case as such:

bcftools view -G -H file.vcf.gz | awk -F'[;=|]' '{for(i=1;i<=NF;i++)if($i=="AA"){print toupper($(i+1));next}}'

And then reinserting them.

This is quite a convoluted way of doing things and I wonder if anyone has a tidier method for doing this?

EDIT:

Here is a single entry from the vcf file (with genotype info hidden):

11  128196  rs576393503 A   G   100 PASS    AC=453;AF=0.0904553;AN=5008;NS=2504;DP=5057;EAS_AF=0.0159;AMR_AF=0.0259;AFR_AF=0.3071;EUR_AF=0.006;SAS_AF=0.0072;AA=g|||;VT=SNP

So here the ancestral allele is g (AA=g) and I need it to be in uppercase so that vcftools recognises it when running the --derived option.

[Pierre Lindenbaum]

I don't get what is this "AA". Show us one line of this vcf please.

[spiral01]

I have edited my question. Thanks.

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk http://lindenb.github.io/jvarkit/VcfFilterJdk.html

java -jar dist/vcffilterjdk.jar -e 'if(!variant.hasAttribute("AA")) return variant; String AA= variant.getAttributeAsString("AA",""); int pipe=AA.indexOf("|"); AA= AA.substring(0,pipe).toUpperCase()+AA.substring(pipe); return new VariantContextBuilder(variant).attribute("AA",AA).make();'

Answer 2

[qing]

Hi spiral01: I want to identify the ancestral allele from my vcf file, but I don't know how to do it. How did you do it?