check rsID of mismatched SNPs by bcftools fixref plugin
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3.3 years ago

I used bcftools fixref plugin to match reference allele with GRCh37. As the result shown below, I have got 18901 unresolved SNPs.

  1. Is there anyway to see the rsID of these unresolved SNPs?
  2. Why are there unresolved SNPs?
  3. What can I do to make these SNPs's reference allele match those in GRCh37?

Result of bcftools fixref

enter image description here

Thank you for any feedback.

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bcftools plugin fixref mismatch • 1.8k views
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Have you not seen the blatant warning given in relation this the operation of this command?

g

[source: https://samtools.github.io/bcftools/howtos/plugin.fixref.html]

Can you elaborate on where you obtained your ensembl.bcf flle or how it was produced? Was it even aligned to hg19 / GRCh37?

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Hi Kevin. Thanks for your comments. I used this unsafe command because when I used the

# Swap the alleles
bcftools +fixref broken.bcf -Ob -o fixref.bcf -- -d -f /path/to/reference.fasta -i All_20151104.vcf.gz

command, the mismatch rate achieved 65%. I think this is because some SNPs in my genotype file are on the reserve strand.

I started to produce the bcf file from PLINK bfiles. I first used PLINK1.9 to recode my bfiles to vcf file, then compressed it to vcf.gz, renamed chromosome 23 -> X etc, and used bcftools sort ensembl.vcf.gz -Ob -o ensembl.bcf and bcftools index ensembl.bcf commands to produce the bcf file and its index. I guess using bcftools +fixref test.bcf -Ob -o output.bcf -- -f ref.fa -m flip -d command can help deal with the SNPs on reserve strand directly.


Update: I used snpflip.py (https://github.com/biocore-ntnu/snpflip) to see the rsID of the unresolved SNPs. It turns out the 18902 SNPs are ambiguous ones and seems it is okay to drop them.

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3.3 years ago

Hey, if you produced the data from PLINK, then it was possibly from a genotyping microarray study, in which case, yes, some of the alleles will be reported on separate strands. For certain protocols, these SNPs are actually removed from analyses, as I allude to here:

Exclude variants not on the coding strand NB This step is only for microarray studies where the probes may only target one strand or the other (sense or non-sense)

[source: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format]

I have to ask: do you definitively have to correct these sites or could you nevertheless proceed with analysis using all sites and just note the issue?

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Hi Kevin. Thanks for your answer. I decide to drop those ambiguous sites and proceed analysis.

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