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missing rs IDs in VCF file using samtools, what is the best tool from GATK?

MasoodaMasooda FallschurchMember

Used samtools, mpileup and got raw.vcf but the rs ID are missing instead there are dots under the rs ID column. Can I process the same file further with a GATK tool and get the snps? or should I process the .sorted.ba, files again with a GATK?

I also want to be able to distinguish somatic vs germline cells, what is best tool for that?


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