Tool for calculating base-level error rate in WGS.
I am seeking a tool to calculate substitution, insertion, deletion error rates at a per-base sequenced level. It has to take a genomic region bed file and vcf files since I don’t want to count germline variants and would like to restrict the analysis to high confidence regions (for instances). I am looking for somethings equivalent to VcfEval from RTG but at base level! And this should take aligned BAM instead of VCFs. Since I am looking for every possible difference between the sequenced reads vs reference + germline varaints. Hopefully, someone can recommend me some tools that are easy to use and fast.
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