How to Fix Error in snpeff
1
0
Entering edit mode
7.3 years ago
misbahabas ▴ 70

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

vcf SNP annotation • 4.1k views
ADD COMMENT
0
Entering edit mode

It says, ERROR_CHROMOSOME_NOT_FOUND 285197

Can you please check your vcf for this?

ADD REPLY
0
Entering edit mode

What do you get if you do:

bcftools view -H yourvariantsfile.vcf | awk '$1=="285197"'

And if you do:

bcftools view -h yourvariantsfile.vcf | awk '$1=="285197"'

(not that in the first case I am asking to show only the variants called, in the second case only the header)

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Then the header of your file is corrupted. How did you generate it?

ADD REPLY
0
Entering edit mode

When i had run both the commands Nothing was seen in my case.

ADD REPLY
0
Entering edit mode
2.7 years ago
Razi • 0

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!

ADD COMMENT
0
Entering edit mode

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 ?!!

ADD REPLY
0
Entering edit mode

I don't know?! So what is your suggestion? Do you think it can be because of gff file?

Thanks!

ADD REPLY
0
Entering edit mode

how you find it is from column 1?

ADD REPLY
0
Entering edit mode

I found the solution. Please look at this link:(https://pcingola.github.io/SnpEff/se_faq/#error_chromosome_not_found-details)

ADD REPLY

Login before adding your answer.

Traffic: 2603 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6