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Question: is the VCF filtering function working?
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gravatar for hschepers
6 weeks ago by
hschepers • 0
hschepers • 0 wrote:

Hi there, I was wondering if the NGS: VCF manipulation: VCFfilter function is actually working. I am trying to filter my VCF file for instances that have an Annotation_Impact = HIGH. (Selected filter type: Info filter (-f). However this returns only 51 header lines, with no results.
In order to see if the filter function is working or if I am typing something wrong, I also tried: DP > 10, DP >100 and DP >1000 these filter only partially. DP>10 and DP>100 give me about the same results, with still DP< 10 or <100 included, whereas DP >1000 gives me over 2900 results, although I am almost sure there is nothing with this sequencing depth in my VCF file. Am I doing something wrong, or is the filter function not functioning? Thanks for your help

Hein
snpsift vcffilter vcftools galaxy • 91 views
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modified 5 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 6 weeks ago by hschepers • 0
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gravatar for Jennifer Hillman Jackson
5 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Try using SnpSift Filter instead.

For "Annotation_Impact = HIGH", the filter criteria would be:

( ANN[*].IMPACT = 'HIGH' )

Query construction help is in that tool's help section (scroll down). The tool SnpSift Extract Fields includes even more help, including a break down what the different fields should be named when constructing a filter (or extracting data into a tabular dataset).

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 5 weeks ago • written 5 weeks ago by Jennifer Hillman Jackson ♦ 25k
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