Software to Filter de novo INDELs
I have VCFs called in trios from GATK haplotype caller. I'm looking for a software tool similar to forestDNM, which takes VCFs as input and determines if putative de novo INDEL calls are true positives (or not).
The caveat is that I do not have access to the BAM files anymore, so the tool should operate only on the VCF file.
Do people have any suggestions or tips on producing a high quality callset of de novo INDELs without querying the BAM file?
Thanks
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