I have gone through filtering variants through
hard-filter from here
My understanding about
VQSR is that the we don't want to combine
INDEL where as they are combined in
In VQSR, we run
INDELand we get
.recalfiles for both snp and indels.
Next, we apply
indels.recalfile to generate
In the next step, we apply
SNPwith vcf input as
indel.recalibrated.vcfand .recal file generated from
This step generate file with
snp.recalibrated.vcf.gzwhich will contain both
INDELas filtered and will be final filtered data from
Is my understanding correct about variant filtering here ?
If this is right how do we deal with
MIXED type ?