MakeGeneticMap with FATAL ERROR Marker # is duplicated

[masen1991]

@WansonChoi Hi ,when i try to use CookHLA on a reference panel build by myself, MakeGeneticMap scripts will go wrong with FATAL ERROR Marker AAC-18_31347808_Rx is duplicated. i check the .markers file it include marks : AAC-18_31347808_R 31347808 P A AAC-18_31347808_x 31347808 P A AAC-18_31347808_Q 31347808 P A AAC-18_31347808_X 31347808 P A AAC-18_31347808_Rx 31347808 P A AAC-18_31347808_RQ 31347808 P A AAC-18_31347808_RX 31347808 P A it may be caused by "AAC-18_31347808_Rx 31347808 P A" and "AAC-18_31347808_RX 31347808 P A" because it seem like Rx/RX make this error. And some times error like this "Error: Duplicate ID 'chr6_31529929_C_T'. " Do u have any suggestion?

[WansonChoi]

@masen0407

Hi, Thank you for your interest in CookHLA.

I guess your expectation is right. I've experienced a very similar error before because of mach's case-insensitive manner.

Can you try removing the marker "AAC-18_31347808_X" and its related markers(ex. "AAC-18_31347808_RX") in your reference panel?

Not only the amino acid residue 'X' is somewhat rare but also genetic distance information of amino acid markers are not critical for HLA imputation.

[masen1991]

@WansonChoi Thank you for your reply. Can you give some advice on removing the marker "AAC-18_31347808_X" and its related markers(ex. "AAC-18_31347808_RX") in my reference panel? it will be some other duplicated marks and i use cat |grep -v "##" to remove from many files such as (.{FRQ.frq,bgl.phased,markers},and i try to use ' plink --bfile .{bed,bim,fam} --export vcf --out new' and then use cat |grep -v "##" to remove marks and plink to change vcf to *bed,bim,fam ) But when i use new file ,Mach go wrong with "FATAL ERROR - Read ZERO reference haplotypes from test.subset.GCchange.haps"

So how to remove duplicated marks from reference panel?

[WansonChoi]

@masen0407

Could you consider sending your reference panel with duplicated markers to me so that I can try to fix them myself? Maybe this way would be faster.

[masen1991]

@WansonChoi
i send my reference panel to your gamil.hope there is some scripts or tools to solver this bug because others day if i try to build some other reference panel it may come again.

[WansonChoi]

@masen0407

I sent the fixed reference panel by email on December 21, 2021. Did you get it well?

[masen1991]

@WansonChoi I have received your email. Sorry for the late reply. The problem has been solved, thank you very much