Calculating allele frequency from VCF file

bio_informatics · 09-29-2014, 02:57 PM

Hi Members,
Please pardon me, if this have been asked previously.

I find no proper answered thread for this.
I have VCF file, with all information. And I need to know allele Frequency.

##FORMAT=<ID=GQX,Number=1,Type=Integer,Description="Minimum of {Genotype quality assuming variant position,Genotype quality assuming non-variant position}">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Filtered basecall depth used for site genotyping">
##FORMAT=<ID=DPF,Number=1,Type=Integer,Description="Basecalls filtered from input prior to site genotyping">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed. For indels this value only includes reads which confidently support each allele (posterior prob 0.999 or higher that read contains indicated allele vs all other intersecting indel alleles)">

Got this information from Isaac Variant caller.

I have information like:

Quote:

chr1 108413 rs200678306 T G 321.00 PASS SNVSB=-29.5;SNVHPOL=6;CSQR=ENSR00001516685|regulatory_region_variant GT:GQ: GQX: DP: DPF:AD 0/1:160:160:59:0:22,37

Is Allele Frequency 22/37

Please help.

bio_informatics · 10-01-2014, 05:57 AM

Please help. Bouncing it.

lupid · 06-30-2016, 09:21 AM

Someone could help in this issue?

sandeep.kolya · 10-25-2016, 08:50 AM

Allele frequency = Alternative_Allele reads (AD) / Total number of reads (DP)

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10-25-2016, 08:50 AM	#4
sandeep.kolya Junior Member Location: India Join Date: Jul 2016 Posts: 1	Allele freuqnecy calculation formula Allele frequency = Alternative_Allele reads (AD) / Total number of reads (DP)

10-01-2014, 05:57 AM	#2
bio_informatics Senior Member Location: USA Join Date: Nov 2013 Posts: 182	Please help. Bouncing it.

06-30-2016, 09:21 AM	#3
lupid Member Location: chile Join Date: Mar 2015 Posts: 54	Someone could help in this issue?