Question: Filtering IonTorrent variant caller VCFs
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gravatar for graeme.thorn
29 days ago by
graeme.thorn30
London, United Kingdom
graeme.thorn30 wrote:

I've got c. 140 VCF files generated by the IonTorrent variant caller pipeline (sequenced using ampliSeq on the comprehensive cancer panel) that I want to process further. However, I'm not sure what filters to apply to the VCFs before grouping them into merged VCFs per group.

As far as I can tell, there are established GATK filtering thresholds, and thresholds for samtools mpileup called variants, but their INFO and FORMAT fields in their vcfs do not match up exactly with those provided by variants called from IonTorrent.

Is it ok to try and translate the GATK thresholds into those used by IonTorrent (as I say there's no exact match between some of the thresholds and values provided by IonTorrent) or is there a known set of hard thresholds somewhere that I could use as a starting point for my filtering?

variants iontorrent vcf • 86 views
ADD COMMENTlink written 29 days ago by graeme.thorn30
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