Is it possible to utilize the 'VariantFiltration' function (v4.1.9.0) to filter a raw VCF file generated using the GATK UnifiedGenotyper function (v3.5)?

Follow

shimijuan

• March 24, 2024 10:06

I use VariantFiltration from GATK v4.1.9 to apply hard filter criteria to an old vcf file created with the UnifiedGenotyper function of GATK v3.5.

The outcome is peculiar, nearly half of the SNPs are flagged as LowQualFilter.  Is the result caused by differences in GATK version or differences in SNP calling functions (UnifiedGenotyper Vs HaplotypeCaller) ?

 

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

0

• 

  Gökalp Çelik

  • March 24, 2024 10:13

  Hi shimijuan

  It is possible to use VariantFiltration tool from a newer version to filter VCFs produced by older versions. 

  For the LowQualFilter can you check whether the unfiltered  VCF file already has that filter applied to some of the variants already? If not one thing that you can do is to try with GATK version 3.x to try applying filtration to see if the result is the same. Unfortunately we cannot help much with older versions of GATK since they are deprecated and no longer supported.

  I hope this helps. 

  0

  Comment actions Permalink

Please sign in to leave a comment.