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I am using bcftools to merge 5000+ vcf files using this command

bcftools merge -l list_of_vcfs.txt

I am getting the following error

 Warning: The row size is too big for FORMAT/PL at chr1:23899810, requires 12204615120 bytes, skipping.
The REF prefixes differ: C vs N (1,1)
Failed to merge alleles at chr1:53128382 in <sample>.vcf.gz

Any help on how to fix this issue would be appreciated.

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  • $\begingroup$ Thanks for the edit @bioinfo_comp and welcome to the site. It's a good sign when the bot message is acted upon, particularly as quickly as you have done. Hope you stick around. $\endgroup$
    – M__
    Jul 25, 2023 at 15:12

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