ythuang0522
commented
2 years ago No. We didn't test Illumina SNPs. It also depends on how you called your SNPs for Illumina and ONT. You may check the evaluation by the PrecisionFDA challenges. If Dragen was used for Illumina-SNP calling, the Illumina accuracy should be better than ONT. But if they were not called by Dragen, I am not sure which one would be better than the other. I suspected only marginal differences. So you may stay with the Illumina SNPs.
tgong1
agolicz
twolinin
Hi longphase team,
Thank you for this helpful software. I'm recently using longphase in our cohort.
We have SNP/indels called from Illumina short-read NGS data. So I have used Illumina SNP VCF + ONT SV VCF + ONT BAM as input for longphase and it has ran pretty well. However, I was wondering the accuracy (or switch rate) of SNP and SV phasing.
I saw you've included a comprehensive benchmarking on GIAB's data in your paper. Have you test the performance of longphase using SNP from short-read NGS data? Will using SNP called from ONT have better performance on phasing from your experience?
Thank you, Tingting