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EichlerLab / smrtsv2

Structural variant caller
MIT License
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Genotyping using short reads? #37

Closed holtgrewe closed 5 years ago

holtgrewe commented 5 years ago

I might be missing something, but I cannot find short or Illumina reads being mentioned in the GENOTYPE.md file.

How could I do genotyping of variants using short-read data?

paudano commented 5 years ago

Sorry for taking so long to respond. My SPAM filters started marking GitHub notifications as junk.

In the first sentence of GENOTYPE.md, "sample alignment files (BAM/CRAM)" are the Illumina short-read samples. In the "Sample table" section, each line is one short-read sample.

If you have FASTQs, then you could place them in an unmapped BAM and run the genotyper on them.

I am updating GENOTYPE.md to make it a little clearer. If you have further questions, feel free to re-open this ticket.