Question: heterozygous genotype in bacterial snp calling
0
gravatar for manjumoorthy95
18 months ago by
manjumoorthy9520 wrote:

I did snp calling for bacterial strains using GATK HaplotypeCaller. The genotypes in the result obtained had, heterozygous variants present in it. Is this possible, since bacteria are haploid.

snp haploid • 532 views
ADD COMMENTlink modified 18 months ago by swbarnes28.9k • written 18 months ago by manjumoorthy9520
0
gravatar for swbarnes2
18 months ago by
swbarnes28.9k
United States
swbarnes28.9k wrote:

It's either an error in mapping due to a bigger discrepancy than a SNP, or it's a repetitive region with slight differences between the loci, or your sample is not clonal. I'd start by eyeballing the regions in IGV, and blast the flanking sequence to see if it's known to be repetitive.

ADD COMMENTlink written 18 months ago by swbarnes28.9k

Ok thank you. Let me try out that way

ADD REPLYlink written 18 months ago by manjumoorthy9520
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 766 users visited in the last hour