plink .bim file missing variant ID
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5.7 years ago

Hello,

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?

Thank you.

plink .bim SNP • 2.0k views
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