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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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cytoBand annotation Bug? #144

Open xiucz opened 3 years ago

xiucz commented 3 years ago

Hi, Version: annovar_2019Oct24

When I use annovar to annotate CNV from CNVnator, I find annovar gives different cytoband results every time

raw cnvnator.vcf:

chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

table_annovar.pl command & results:

annovar_2019Oct24/annovar/table_annovar.pl  \
--outfile cnvnator.annovar \
--vcfinput cnvnator.vcf \
--buildver hg19 /local_data1/MED/database/hg19/humandb --otherinfo --remove -protocol cytoBand,dgvMerged -operation r,r

#the first time 
chr17   1   18960000    0   -   17p13.1-p12 0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

#the second time（repeat above command）
chr17   1   18960000    0   -   17p11.2-p12 0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

#the third time(repeat above command all the same)
chr17   1   18960000    0   -   17p12-p11.2 0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

#the fourth time
chr17   1   18960000    0   -   17p13.1-p11.2   0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

Well... I change table_annovar.pl to annotate_variation.pl annotate_variation.pl command & result:

annovar_2019Oct24/annovar/annotate_variation.pl -regionanno -build hg19 -dbtype cytoBand annovar.avinput /local_data1/MED/database/hg19/humandb # the annovar.avinput file from the temp file above

#first time
cytoBand    17p12-p13.1 chr17   1   18960000    0   -   0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

#second time
cytoBand    17p12-p13.1 chr17   1   18960000    0   -   0.5 .   .   chr17   1   CNVnator_del_9  A   <DEL>   .   PASS    END=18960000;SVTYPE=DEL;SVLEN=-18960000;IMPRECISE;natorRD=0.60347;natorP1=8.40572e-15;natorP2=3.02227e-69;natorP3=8.40572e-15;natorP4=3.02227e-69;natorQ0=0.012191  GT:CN   0/1:1

#third time
same result

and cytoband file

chr17   0   3300000 p13.3   gneg
chr17   3300000 6500000 p13.2   gpos50
chr17   6500000 10700000    p13.1   gneg
chr17   10700000    16000000    p12 gpos75
chr17   16000000    22200000    p11.2   gneg
chr17   22200000    24000000    p11.1   acen
chr17   24000000    25800000    q11.1   acen
chr17   25800000    31800000    q11.2   gneg

And according to ISCN, The correct result should not be p11.2-p13.3? After my check, I am a little puzzled. Is this this a bug?

Thanks for your reply. Xiucz.

lgmgeo commented 3 years ago

Your interpretation seems correct Xiucz. For the deletion chr17:1-18,960,000, the UCSC genome browser returns the cytoband chr17 (p13.3-p11.2) as shown below:

image