error in the genotyping ?
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mette Joergensen
Mar 31, 2017, 7:23:58 PM3/31/17
to cortex_var
I have had an example where I have been genotyping 6 bacteria samples and I were using the reference in calling.
Cortex reported a long insertion (215bp) and 5 samples had the genotype 1/1 and one sample the genotype 0/0. The strange thing is that when I blasted the insertion against the reference genome and the genomes with the genotype 1/1 the sequence was found with 100% identity and 100% coverage in both the reference and the samples. So shouldn't it have a been deletion and the genotypes the opposite ? Or do I misunderstand something ?
Best,
Mette
Cortex reported a long insertion (215bp) and 5 samples had the genotype 1/1 and one sample the genotype 0/0. The strange thing is that when I blasted the insertion against the reference genome and the genomes with the genotype 1/1 the sequence was found with 100% identity and 100% coverage in both the reference and the samples. So shouldn't it have a been deletion and the genotypes the opposite ? Or do I misunderstand something ?
Best,
Mette
Zamin Iqbal
Mar 31, 2017, 7:34:49 PM3/31/17
to cortex_var
Hi Mette
Zam
It's a little hard to say, but that does sound like a bug.How were you calling? Bubble caller or PD?
Zam
mette Joergensen
Apr 10, 2017, 10:23:49 AM4/10/17
to cortex_var
Both bc and pd
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