MutScan
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the latest mutscan cannot be work with VEP-annoated vcf ?
Command example with vep-annotated VCF as input:
mutscan -1 R1.fq.gz -2 R2.fq.gz -m VEP.vcf -r ref.a
outputs:
No mutation to be scanned
Your VCF contains no valid records
So I conclude that there must be something is wrong. However, when raw vcf is used, no such warning but empty results.