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 completion
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
Thanks
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written
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misbahabas •
Hi,
I have the same issue. Would you please help me to solve this?
I ran this command:
java -Xmx4g -jar snpEff.jar -c snpEff.config -v BF BF.vcf.gz > BF.ann.vcf
And Got this error:
"RRORS: Some errors were detected Error type: ERROR_CHROMOSOME_NOT_FOUND Number of errors: 8419432"
I check these: bcftools view -H BF.vcf.gz | awk '$1=="8419432"' bcftools view -h BF.vcf.gz | awk '$1=="8419432"'
and there was no answer!
Would you please help me? Thanks!
Number of errors: 8419432"
it's a number of errors. Why on earth would you find the number of errors in the column 1 of a VCF ?!!
I found the solution. Please look at this link:(https://pcingola.github.io/SnpEff/se_faq/#error_chromosome_not_found-details)
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It says,
ERROR_CHROMOSOME_NOT_FOUND 285197Can you please check your vcf for this?
What do you get if you do:
And if you do:
(not that in the first case I am asking to show only the variants called, in the second case only the header)
when i run first command It give result like that
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
and in second case are also same
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
Then the header of your file is corrupted. How did you generate it?
When i had run both the commands Nothing was seen in my case.