error ,,, file.vcf --> file snpEff.vcf

Question

[tranthach90]

hi everyone. help me!

I run

VarScan > rice-snp.vcf

and I want run with snpEff tools but error!

./snpEff$ java -jar snpEff.jar rice7 rice-snp.vcf > s.eff.vcf

ERRORS: Some errors were detected
Error type      Number of errors
ERROR_CHROMOSOME_NOT_FOUND      330650

Can anybody help me...thanks all.

[tranthach90]

# format file input.vcf

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    Sample1
LOC_Os01g01070    1254    .    A    G    .    PASS    ADP=13;WT=0;HET=0;HOM=1;NC=0   
LOC_Os01g01070    3850    .    A    G    .    PASS    ADP=11;WT=0;HET=0;HOM=1;NC=0    
LOC_Os01g01070    4240    .    C    T    .    PASS    ADP=12;WT=0;HET=0;HOM=1;NC=0   
LOC_Os01g01080    2809    .    T    C    .    PASS    ADP=11;WT=0;HET=0;HOM=1;NC=0   
LOC_Os01g01090    435    .    G    A    .    PASS    ADP=15;WT=0;HET=1;HOM=0;NC=0   
..............

[Devon Ryan]

Is the rice7 database one you made yourself or one of the premade ones?

[tranthach90]

Yes. I made for my group and it is part of the project.

[Devon Ryan]

Does it have the same chromosome names? My guess would be not.

Answer 1

[Pablo]

Three suggestions:

1. Make sure the input file is really VCF

2. Run SnpEff using verbose mode (-v) and it will show all chromosome names and lengths

   $ java -Xmx4g -jar snpEff.jar -v rice7 test.vcf
   
   # Chromosomes names [sizes]  :
   #               '1' [43270923]
   #               '3' [36413819]
   #               '2' [35937250]
   #               '4' [35502694]
   #               '6' [31248787]
   #               '5' [29958434]
   #               '7' [29697621]
   #               '11' [29021106]
   #               '8' [28443022]
   #               '12' [27531856]
   #               '10' [23207287]
   #               '9' [23012720]
   #               'Un' [633585]
   #               'Sy' [592136]
   

3. If that doesn't work, send me some sample data (http://snpeff.sourceforge.net/about.html#help ) and I'll try to look into it

Cheers

Pablo

[tranthach90]

orror!

name chromosome of file input.vcf is "LOC_Os01g01070..."

and name chromosome of data rice7 is:

# Chromosomes names [sizes]  :
#               '1' [43270923]
#               '3' [36413819]
#               '2' [35937250]
#               '4' [35502694]
#               '6' [31248787]
#               '5' [29958434]
#               '7' [29697621]
#               '11' [29021106]
#               '8' [28443022]
#               '12' [27531856]
#               '10' [23207287]
#               '9' [23012720]
#               'Un' [633585]
#               'Sy' [592136]

[Devon Ryan]

Well there's your problem.

[tranthach90]

I'm sorry but My major is biology research and this is my problem.

[Devon Ryan]

Many of us are "reformed biologists" :) It looks like you aligned to the transcriptome rather than the genome, since LOC_Os01g01070 is a transcript (apparently of a transcription factor).