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alekseyzimin / masurca

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superReadSequences for Variant calling #169

Open kokyriakidis opened 4 years ago

kokyriakidis commented 4 years ago

Hi @alekseyzimin!

I have illumina + HiFi data. Can I do variant calling with superReadSequences produced by these two types of data?

Is some information lost during this proccess? Can I map these superReadSequences with BWA

alekseyzimin commented 4 years ago

You can. I recommend mapping the super-reads with nucmer and using the delta2vcf.pl script in the 3.4.2 version.

delta2vcf.pl< out.delta > out.vcf