what is the differences between filtered and unfiltered VCF files

Question

[stat.1405]

There are two different type of vcf files, Filtered record and unfiltered.

What is the difference between them?

Answer 1

[Ashutosh Pandey]

A normal practice after variant calling is filtering for the low quality variants. Variant callers like GATK UnifiedGenotyper assign quality scores to each variant. Normally, researchers choose some threshold and discard or flag the variants with lower quanlity scores as FAILED. Additional parameters such as minimum number of supporting reads, mapping quality of supporting reads, proximity to known indels can also be used to flag the variant as PASS or FAIL. The seventh column (FILTER ) of VCF file is used to display this information. VCF format allows any alphanumeric string for column seven. So you can add any relevant information about your variant in that column. Now coming back to your question, if a filtering has already been applied to a vcf file then it will be called filtered vcf file and vice-versa.

Answer 2

[Matt Shirley]

One has been poured through cheesecloth or carbon, and the other one has a more full body and aroma.

:)

[stat.1405]

thanks Matt