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Hi @Geraldine_VdAuwera and @Sheila, It has been several years since this article was originally was posted. You described this possibility: "We also plan to add functionality to process DNAseq and RNAseq data from the same samples simultaneously"…
@Sheila I have submitted the bug report called "GATK_bugreport_dsap.tar". Thanks!
@Geraldine_VdAuwera I am not sure how to go about that. I used the "head" unix command to isolate the first 25,000 lines, about ~24,000 of which are the commented VCF IDs and scaffold numbers. And it did not work anyway. The first error I …
Thanks @esalvi, I have tried that as well, but plink tells me "missing header line in .vcf file" and I do not know what it could be as it it looks like a normal VCF. My problem might be that I am dealing with >24,000 scaffolds from a nonmodel org…