Multiple alleles in REF and ALT in VCF file
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17 months ago
Volka ▴ 170

Hi all, I am looking at some data in my VCF file and came across this line below:

20      62855516        20:62855516:GC:AC       GC      AC      .       .       PR;AC=8;AN=70   GT      0/0     0/0     0/0     0/0     0/1     0/1     0/1   0/0      0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/0     0/1     0/0     0/0     0/0     0/0     0/1     0/1     0/1     0/0     0/0   0/0      0/1     0/0     0/0     0/0     0/0     0/0     0/0

My question is, is this considered a multiallelic site? How should I handle this entry? I am also looking to compare sites with another VCF, and the equivalent position in the other VCF has G in REF and A in ALT, is there a way to clean the data to consider only the first allele for this entry?

I've tried to remove/fix these entries with bcftools view -m2 -M2 -v snps and bcftools norm -m -any but it doesn't seem to catch it.

Thanks.

vcf allele indel bcftools vcftools • 526 views
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Instead of removing, try decomposing vcfs with Vt. Refer to the decompose biallelic block substitutions section here: https://genome.sph.umich.edu/wiki/Vt

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