three g-strip questions

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭


My workflow is for unrelated individuals, in model organism, with many small unmapped contigs high in heterochromatin.

  1. No genotype calls are being generated in final genotyped vcf. Lots of LQ indicated in genotype fields, and few PASS in the filter field. Currently using 9 inds so am increasing this number to improve things. Does this sound the most likely solution or could it be something else?

  2. Does the alternate allele stage have to be included prior to genotyping, or is this not useful unless CNV/deletions are known previously in the same population?

  3. It's documented that the whole genome should be used but I expect that the unmapped, heterochromatic scaffolds will poor data quality. Will GS run properly if these are excluded, (just by using -L to state the required chromosomes?


Will Gilks


Best Answer


  • Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

    @bhandsaker Thanks for getting back to me.

    1. Got it but have other stuff to fix. (Deletion pipeline atm. 20-30X, all females)

    2. Got it. (Reads are long-ish - will exclude alt allele stage).

    3. Got it. (Preprocessing on as much of genome as possible.., discovery all or any of preprocessing regions.)

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