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?