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


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 • 1.0k views
ADD COMMENTlink written 2.0 years ago by genomics Newbie20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 823 users visited in the last hour