First I generated a pileup from my BAM sequences and converted the pileup to vcf. samtools mpileup -uf ucsc.hg19.fasta sample_rna-seq.bam | bcftools call -mv -Oz > calls.vcf.gz
I then used PLINK to make the bed, bim and fam files. Although the format was correct, the Variant ID was missing from the bim file.
Question: Is a blank bim file variant ID appropriate for tumor samples? Could the missing SNP be a result of not "interacting" with the dbSNP database?