Variant Filtration - FS and SOR are not supported

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Khalil Jahed

• January 22, 2020 22:01
• Edited

Hi,

The FS and SOR variant filtration options do not work. Are they still active? NOTE: AB and MQ work using the same command. GATK/4.14.1 was used. 

Command lines: 

gatk VariantFiltration \
 -R ref.fasta \
 -V input.vcf \
 -O output.vcf \
 --filter-name "my_filter1" \
 --filter-expression "FS > 60" \
 --filter-name "my_filter2" \
 --filter-expression "SOR > 3"

 

Error file is located here

 

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• Official comment

  

  Bhanu Gandham

  • January 24, 2020 00:41

  This is happening because you wrote the threshold values as integers but some of the annotations can have decimals, so the evaluation fails. This limitation is documented in the filtering docs. You can fix this by using the decimal notation instead for the failing annotations. For example, for QD you would make the threshold value 2.0 instead of 2.

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