Beagle conform-gt error

Question

[kstafford32]

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?

[4galaxy77]

Please could you edit your question to show the full command you have used - it helps to know what you passed to the match argument. Either way, you need to remove markers that have either duplicated positions or IDs. Something like bcftools norm will do the trick for you.