Question: plink .bim file missing variant ID
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gravatar for genomics Newbie
9 months ago by
genomics Newbie20 wrote:

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.

snp plink .bim • 495 views
ADD COMMENTlink written 9 months ago by genomics Newbie20
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