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  • How to Fix Error in snpeff

    Asslamu Alikum

    I am using snpeff to annotate vcf files, When I run command it gives some errors and warnings

    " java -Xmx4g -jar snpEff.jar CanFam3.1.75 -v /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/DQ1.g.vcf > DQ1.ann.vcf"

    It give error at the end of complition

    ERRORS: Some errors were detected

    Error type Number of errors

    ERROR_CHROMOSOME_NOT_FOUND 285197

    WARNINGS: Some warning were detected Warning type Number of warnings INFO_REALIGN_3_PRIME 6443 WARNING_TRANSCRIPT_INCOMPLETE 277 WARNING_TRANSCRIPT_NO_START_CODON 678825 WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME 943 WARNING_TRANSCRIPT_NO_STOP_CODON 499400 WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME 346

    Is it effect on the results? I don't know how to fix it.

    Please tell me about it

    thankx

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