Question

Understanding VCF abbreviations

1

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6.0 years ago

aharnishi02 ▴ 80

My VCF contains the following:

DP=33;VDB=0.0951013;SGB=-0.691153;RPB=0.527181;MQB=0.00139564;MQSB=0.999702;BQB=0.328758;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=4,5,8,10;MQ=47

and

GT:NR:DP:SR:VR:VA:SB:ABQ:AMQ: 1/0:468.73038:23:65.22:65.22:.:24.93:33.53:220.13

Could you please help me get the expansions for these abbreviations??

next-gen alignment • 3.1k views

ADD COMMENT • link updated 17 months ago by Cyriac Kandoth 6.0k • written 6.0 years ago by aharnishi02 ▴ 80

score 3 · Answer 1 · 2018-05-02

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6.0 years ago

Pierre Lindenbaum 161k

Could you please help me get the expansions for these abbreviations??

they're defined in the VCF header.

e.g:

##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

ADD COMMENT • link 6.0 years ago by Pierre Lindenbaum 161k

score 1 · Answer 2 · 2018-05-02

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6.0 years ago

finswimmer 16k

Hello,

have a look at the header entries of your vcf file (those lines starting with ## at the top of the file). All fields are described there.

If you doesn't understand a description feel free to ask.

fin swimmer

ADD COMMENT • link 6.0 years ago by finswimmer 16k

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Hi,

Thank you for your reply, the problem I am facing is I used third party software to obtain the VCF ( since I dont have a bioinfomatics background), I found these abbreviations in the .csv output i obtained after running the VCF on wANNOVAR. So i am not reading the VCF file, but the .csv file

ADD REPLY • link 6.0 years ago by aharnishi02 ▴ 80

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So i am not reading the VCF file, but the .csv file

it's like trying to re-create a cow from a steak

ADD REPLY • link 6.0 years ago by Pierre Lindenbaum 161k

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Haha, True!!.. but that's where I am!! Anyway, Thank you. :)

ADD REPLY • link 6.0 years ago by aharnishi02 ▴ 80

score 0 · Answer 3 · 2018-05-02

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6.0 years ago

JJ ▴ 680

Have a look at this page - I think they neatly explain various entries.

ADD COMMENT • link 6.0 years ago by JJ ▴ 680

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I wonder why you're pointing to the 1000Genome VCF v4.0 resource instead of the official VCF v4.2 or v4.3 documentation

ADD REPLY • link 6.0 years ago by Ram 43k

score 0 · Answer 4 · 2022-11-19

I encountered such a VCF in a support thread, and I still have no idea what third party tool generates these. But the VCF header describes these fields.

##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="Read Depth">
##FORMAT=<ID=SR,Number=1,Type=Float,Description="Supporting reads">
##FORMAT=<ID=VR,Number=1,Type=Float,Description="Variant reads">
##FORMAT=<ID=VA,Number=1,Type=Integer,Description="1=Variant ambiguous, Genotype at this location is not clear, otherwise VA=0">
##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand bias">
##FORMAT=<ID=ABQ,Number=1,Type=Float,Description="Average base quality">
##FORMAT=<ID=AMQ,Number=1,Type=Float,Description="Average mapping quality">

Also peculiar is that SR (Supporting reads) and VR (Variant reads) are not whole numbers and instead look like VAF, Variant Allele Fraction as a percentage value.