Question: Software to Filter de novo INDELs
0
gravatar for QVINTVS_FABIVS_MAXIMVS
2.5 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

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

software indels de novo • 584 views
ADD COMMENTlink written 2.5 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1514 users visited in the last hour