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Question: Thresholds to filter out variants from vcf file
0
gravatar for abedkurdi10
4.2 years ago by
abedkurdi10 • 30
abedkurdi10 • 30 wrote:

Hi all. I would like to ask what are thresholds used to filter out variants from VCF file ? if provided, are they used as standards or it depends ?

I appreciate any help. Thank you.
thresholds filtering vcf • 2.2k views
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modified 4.2 years ago by Ron • 1.0k • written 4.2 years ago by abedkurdi10 • 30
3
gravatar for WouterDeCoster
4.2 years ago by
WouterDeCoster ♦ 45k
Belgium
WouterDeCoster ♦ 45k wrote:

For that see the following pages from GATK:

Obviously there is no solution to all problems but these guidelines will hopefully put you on the right track.
ADD COMMENT • link written 4.2 years ago by WouterDeCoster ♦ 45k

what if I need to annotate them using vcftools, is there any thresholds to follow like MinDP, QUAL, GQ ?

ADD REPLY • link written 4.2 years ago by abedkurdi10 • 30

Have you read the pages I linked?

ADD REPLY • link written 4.2 years ago by WouterDeCoster ♦ 45k

yes, but GATK has different attributes for filtration, they are based on calculations...

ADD REPLY • link written 4.2 years ago by abedkurdi10 • 30
1

I don't understand why you would need to annotate them using vcftools and can't use GATK filter guidelines, but sure, go ahead.

ADD REPLY • link written 4.2 years ago by WouterDeCoster ♦ 45k
1
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