Can I Get Ad (Allelic Depth) Information In Vcf File With Samtools ?

Question

[Scubnoucca]

When I search for SNP with Samtools mpileup, in the FORMAT field from the final VCF file, I have :

GT : PL : GQ

GT : Genotype
PL : List of Phred-scaled genotype likelihoods
GQ : Genotype Quality

Is it possible to add the Allelic Depth information (AD) in the VCF file ? Is there an option for this ?

GT : AD : PL : GQ

Thanks

Answer 1

[Aaron H]

If you want to add the information to the FORMAT field, I would use GATK's VariantAnnotator

$ java -Xmx2g -jar /path/to/GenomeAnalysisTK.jar -R /path/to/ref.fasta -V input.vcf -T VariantAnnotator -A DepthPerAlleleBySample -o annotated.vcf

Answer 2

[Pierre Lindenbaum]

I don't think you can do this with samtools (tested with 0.1.17):

$ find ./ -name  "*.[ch]" -exec grep '"GT"' '{}' ';' | wc -l
6
$ find ./ -name  "*.[ch]" -exec grep '"PL"' '{}' ';' | wc -l
18
$ find ./ -name  "*.[ch]" -exec grep '"GQ"' '{}' ';' | wc -l
5
$ find ./ -name  "*.[ch]" -exec grep '"AD"' '{}' ';' | wc -l
0 ##zero <-------