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3 hours ago by

Hi,

I ran a beagle conform-gt script to fix my snpflip topmed qc imputation error. Conform-gt gave this error as well as many other similar ones for different chromosomes:

 Exception in thread "main" java.lang.IllegalArgumentException: Duplicate marker [OUTDIR/conformgt_HG38_Ref_2/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz]: 1    7623266 rs554779128  T       TTGAA
    at conform.ConformMarkers.<init>(ConformMarkers.java:62)
    at conform.ConformMain.<init>(ConformMain.java:108)
    at conform.ConformMain.main(ConformMain.java:97)

Files were not uploaded to my out folder. From reading this error message above, I know there are duplicates I have to remove, but I am unsure where. Most posts here and elsewhere do not contain the "conform.conformMarkers" portion in their error. Does this mean that I have duplicates in my reference file and not in my gt files? This was an hg38 reference source I obtained online, so how can this be?



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