Mutect2 md5 error

Using the standard mutect2 commands from the docs I get the error seen below. My reference file dictionaries were all made automatically from mutect version 1.4. Is there a workaround for this md5 problem. I tried an awk command to take out the m5 column from the fast.dict file, but that didnt work. Is there a flag that I'm not seeing to avoid this MD5 column check because for my purposes if the length is the same its likely that they are the same contig? Any help would be greatly appreciated.

ERROR MESSAGE: Input files reads and reference have incompatible contigs. Please see more information. Error details: Found contigs with the same name but different lengths or MD5s:
ERROR contig reads is named 3 with length 198022430 and MD5 fdfd811849cc2fadebc929bb925902e5
ERROR contig reference is named 3 with length 198022430 and MD5 641e4338fa8d52a5b781bd2a2c08d3c3.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @eritch,

    The MD5 issue is an overreaction that was introduced by accident in the last release. We'll fix it in the near future; in the meantime you can disable the dictionary checking by using the -U ALLOW_SEQ_DICTIONARY_INCOMPATIBILITY argument.

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