Question: what is the differences between filtered and unfiltered VCF files
0
gravatar for stat.1405
3.6 years ago by
stat.140510
uk
stat.140510 wrote:

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

What is the differents between them. 

snp vcftools next-gen • 1.4k views
ADD COMMENTlink modified 3.6 years ago by Matt Shirley7.9k • written 3.6 years ago by stat.140510
5
gravatar for Ashutosh Pandey
3.6 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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. 

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Ashutosh Pandey11k
1
gravatar for Matt Shirley
3.6 years ago by
Matt Shirley7.9k
Cambridge, MA
Matt Shirley7.9k wrote:

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

:)

ADD COMMENTlink written 3.6 years ago by Matt Shirley7.9k

thanks Matt

ADD REPLYlink written 3.6 years ago by stat.140510
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