This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Hard filtering RNA-seq data
I used the GATK Best Practices workflow for variant calling on RNAseq, but I have a question regarding the filter recommendations for the variant filtering step. According to your workflow, you recommend using the filters '–window 35, –cluster 3, FS > 30.0 and QD < 2.0'. However, in https://software.broadinstitute.org/gatk/documentation/article.php?id=3225, the recommended arguments to use with VariantFiltration for SNPs are 'QD < 2.0, MQ < 40.0, FS > 60.0, SOR > 3.0, MQRankSum > -12.5 and ReadPosRankSum < -8.0'. Is this more stringent option only recommended for DNA-seq data? What is the reason for the different recommendations?