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.
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abedkurdi10 •
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.
what if I need to annotate them using vcftools, is there any thresholds to follow like MinDP, QUAL, GQ ?
Have you read the pages I linked?
yes, but GATK has different attributes for filtration, they are based on calculations...
I don't understand why you would need to annotate them using vcftools and can't use GATK filter guidelines, but sure, go ahead.
Some posts you may want to refer:
What are good settings for filtering VCF files?
How Do You Usually Filter Variant Calling Results?
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