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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
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