Can I Get Ad (Allelic Depth) Information In Vcf File With Samtools ?
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10.3 years ago
Scubnoucca • 0

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

samtools allele vcf • 5.2k views
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Entering edit mode
10.2 years ago
Aaron H ▴ 170

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

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Entering edit mode
10.3 years ago

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 <-------
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