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Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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Exonic variants are in the variant_function while the exonic_variant_function is empty. #97

Open Jiny000 opened 4 years ago

Jiny000 commented 4 years ago

Hi, I used annovar with below command to annotate the result of pbsv:

/share/home/annovar/convert2annovar.pl -format vcf4 sample.vcf >sample.annovar
/share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE
intergenic      TraesCS1D02G001600(dist=16666),TraesCS1D02G001700(dist=12310)   chr1D   434819  434819  A       0       het     .       30
intergenic      TraesCS1D02G001600(dist=26665),TraesCS1D02G001700(dist=2311)    chr1D   444818  444818  T       0       het     .       28
exonic  TraesCS1D02G001700      chr1D   448395  448395  T       0       het     .       15
intergenic      TraesCS1D02G002200(dist=13802),TraesCS1D02G002300(dist=19271)   chr1D   528898  528898  G       0       het     .       9
intergenic      TraesCS1D02G002200(dist=14929),TraesCS1D02G002300(dist=18144)   chr1D   530025  530025  T       0       het     .       5
intergenic      TraesCS1D02G002200(dist=21479),TraesCS1D02G002300(dist=11594)   chr1D   536575  536575  T       0       het     .       21
……

It is clear that there are exonic variant in the sample.variant_function file.However,the related sample.exonic_variant_function file is empty.Why? The annovar input file is below:

chr1D   33198   33198   G       0       het     .       6
chr1D   33210   33210   T       0       het     .       8
chr1D   33952   33952   T       0       het     .       5
chr1D   77394   77394   C       0       het     .       14
chr1D   291865  291865  A       0       het     .       17
chr1D   291881  291881  C       0       het     .       23
……

I have tried use awk '$3=$3+1,OFS="\t"' sample.annovar and awk '$3=$3+1,OFS="\t"' sample.annovar |awk '$5="T",OFS="\t"' |awk '$4="A",OFS="\t"' to generate different fake annovar files.But all of sites in them are attributed to invalid_input.I wonder if it is a bug or it is due to the input file wrong I used. Here is the log file:

ANNOVAR Version:
        $Date: 2018-04-16 00:43:31 -0400 (Mon, 16 Apr 2018) $
ANNOVAR Information:
        For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/
ANNOVAR Command:
        /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE
ANNOVAR Started:
        Thu Jun 25 21:37:48 2020
NOTICE: Output files were written to sample.variant_function, sample.exonic_variant_function
NOTICE: Reading gene annotation from /share/home/SAMPLE/SAMPLE_refGene.txt ... Done with 298774 transcripts (including 0 without coding sequence annotation) for 269428 unique genes
NOTICE: Processing next batch with 109504 unique variants in 109504 input lines

Sincerely, Jingyao

kaichop commented 4 years ago

use table_annovar. This is NOT a vcf file, and you should never treat it as a VCF file. Read quick startup guide thoroughly and read the website thoroughly.

On Thu, Jun 25, 2020 at 10:46 AM Jiny000 notifications@github.com wrote:

Hi, I used annovar with below command to annotate the result of pbsv:

/share/home/annovar/convert2annovar.pl -format vcf4 sample.vcf >sample.annovar

/share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE

intergenic TraesCS1D02G001600(dist=16666),TraesCS1D02G001700(dist=12310) chr1D 434819 434819 A 0 het . 30

intergenic TraesCS1D02G001600(dist=26665),TraesCS1D02G001700(dist=2311) chr1D 444818 444818 T 0 het . 28

exonic TraesCS1D02G001700 chr1D 448395 448395 T 0 het . 15

intergenic TraesCS1D02G002200(dist=13802),TraesCS1D02G002300(dist=19271) chr1D 528898 528898 G 0 het . 9

intergenic TraesCS1D02G002200(dist=14929),TraesCS1D02G002300(dist=18144) chr1D 530025 530025 T 0 het . 5

intergenic TraesCS1D02G002200(dist=21479),TraesCS1D02G002300(dist=11594) chr1D 536575 536575 T 0 het . 21

……

It is clear that there are exonic variant in the sample.variant_function file.However,the related sample.exonic_variant_function file is empty.Why? The annovar input file is below:

chr1D 33198 33198 G 0 het . 6

chr1D 33210 33210 T 0 het . 8

chr1D 33952 33952 T 0 het . 5

chr1D 77394 77394 C 0 het . 14

chr1D 291865 291865 A 0 het . 17

chr1D 291881 291881 C 0 het . 23

……

I have tried use awk '$3=$3+1,OFS="\t"' sample.annovar and awk '$3=$3+1,OFS="\t"' sample.annovar |awk '$5="T",OFS="\t"' |awk '$4="A",OFS="\t"' to generate different fake annovar files.But all of sites in them are attributed to invalid_input.I wonder if it is a bug or it is due to the input file wrong I used. Here is the log file:

ANNOVAR Version:

    $Date: 2018-04-16 00:43:31 -0400 (Mon, 16 Apr 2018) $

ANNOVAR Information:

    For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/

ANNOVAR Command:

    /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE

ANNOVAR Started:

    Thu Jun 25 21:37:48 2020

NOTICE: Output files were written to sample.variant_function, sample.exonic_variant_function

NOTICE: Reading gene annotation from /share/home/SAMPLE/SAMPLE_refGene.txt ... Done with 298774 transcripts (including 0 without coding sequence annotation) for 269428 unique genes

NOTICE: Processing next batch with 109504 unique variants in 109504 input lines

Sincerely, Jingyao

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/97, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OHI7BO2UGLD5EWAT3LRYNPOFANCNFSM4OIOGEOA .

Jiny000 commented 4 years ago

Hi, I'm sorry my explaination is not clear enough.I had  converted vcf file to annovar file by convert2annovar.pl,and what I supplied above is the annovar file,which is the result of convert2annovar.pl.In fact,I have series of vcf files,and all can be transfer into annovar file by convert2annovar.pl successfully.With using annotate_variation.pl,all can be annotated with variant_function.file,but some of their related exonic-variant-function files are empty while there are exnoic sites in variant_function.file.I wonder why some  exonic-variant-function files are empty.

As for table_annovar.pl,I will try it if it still can not be solved. Wait for your reply.:)

------------------ 原始邮件 ------------------ 发件人: "Kai Wang"<notifications@github.com>; 发送时间: 2020年6月25日(星期四) 晚上10:54 收件人: "WGLab/doc-ANNOVAR"<doc-ANNOVAR@noreply.github.com>; 抄送: "李竞尧"<821357094@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [WGLab/doc-ANNOVAR] Exonic variants are in the variant_function while the exonic_variant_function is empty. (#97)

use table_annovar. This is NOT a vcf file, and you should never treat it as a VCF file. Read quick startup guide thoroughly and read the website thoroughly.

On Thu, Jun 25, 2020 at 10:46 AM Jiny000 <notifications@github.com> wrote:

> Hi, > I used annovar with below command to annotate the result of pbsv: > > /share/home/annovar/convert2annovar.pl -format vcf4 sample.vcf >sample.annovar > > /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE > > > intergenic TraesCS1D02G001600(dist=16666),TraesCS1D02G001700(dist=12310) chr1D 434819 434819 A 0 het . 30 > > intergenic TraesCS1D02G001600(dist=26665),TraesCS1D02G001700(dist=2311) chr1D 444818 444818 T 0 het . 28 > > exonic TraesCS1D02G001700 chr1D 448395 448395 T 0 het . 15 > > intergenic TraesCS1D02G002200(dist=13802),TraesCS1D02G002300(dist=19271) chr1D 528898 528898 G 0 het . 9 > > intergenic TraesCS1D02G002200(dist=14929),TraesCS1D02G002300(dist=18144) chr1D 530025 530025 T 0 het . 5 > > intergenic TraesCS1D02G002200(dist=21479),TraesCS1D02G002300(dist=11594) chr1D 536575 536575 T 0 het . 21 > > …… > > > It is clear that there are exonic variant in the sample.variant_function > file.However,the related sample.exonic_variant_function file is empty.Why? > The annovar input file is below: > > chr1D 33198 33198 G 0 het . 6 > > chr1D 33210 33210 T 0 het . 8 > > chr1D 33952 33952 T 0 het . 5 > > chr1D 77394 77394 C 0 het . 14 > > chr1D 291865 291865 A 0 het . 17 > > chr1D 291881 291881 C 0 het . 23 > > …… > > > I have tried use awk '$3=$3+1,OFS="\t"' sample.annovar and awk > '$3=$3+1,OFS="\t"' sample.annovar |awk '$5="T",OFS="\t"' |awk > '$4="A",OFS="\t"' to generate different fake annovar files.But all of > sites in them are attributed to invalid_input.I wonder if it is a bug or it > is due to the input file wrong I used. > Here is the log file: > > ANNOVAR Version: > > $Date: 2018-04-16 00:43:31 -0400 (Mon, 16 Apr 2018) $ > > ANNOVAR Information: > > For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/ > > ANNOVAR Command: > > /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE > > ANNOVAR Started: > > Thu Jun 25 21:37:48 2020 > > NOTICE: Output files were written to sample.variant_function, sample.exonic_variant_function > > NOTICE: Reading gene annotation from /share/home/SAMPLE/SAMPLE_refGene.txt ... Done with 298774 transcripts (including 0 without coding sequence annotation) for 269428 unique genes > > NOTICE: Processing next batch with 109504 unique variants in 109504 input lines > > > > > Sincerely, > Jingyao > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <https://github.com/WGLab/doc-ANNOVAR/issues/97&gt;, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ABNG3OHI7BO2UGLD5EWAT3LRYNPOFANCNFSM4OIOGEOA&gt; > . >

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

kaichop commented 4 years ago

Do not use convert2annovar (or annotate_variation), unless you are already an expert on annovar and understand it well. You can directly annotate your input file (regardless of what format it is), using table_annovar.pl Read the quick start-up guide first, before doing anything else.

On Thu, Jun 25, 2020 at 9:08 PM Jiny000 notifications@github.com wrote:

Hi, I'm sorry my explaination is not clear enough.I had  converted vcf file to annovar file by convert2annovar.pl,and what I supplied above is the annovar file,which is the result of convert2annovar.pl.In fact,I have series of vcf files,and all can be transfer into annovar file by convert2annovar.pl successfully.With using annotate_variation.pl,all can be annotated with variant_function.file,but some of their related exonic-variant-function files are empty while there are exnoic sites in variant_function.file.I wonder why some  exonic-variant-function files are empty.

As for table_annovar.pl,I will try it if it still can not be solved. Wait for your reply.:)

------------------ 原始邮件 ------------------ 发件人: "Kai Wang"<notifications@github.com>; 发送时间: 2020年6月25日(星期四) 晚上10:54 收件人: "WGLab/doc-ANNOVAR"<doc-ANNOVAR@noreply.github.com>; 抄送: "李竞尧"<821357094@qq.com>;"Author"<author@noreply.github.com>;

主题: Re: [WGLab/doc-ANNOVAR] Exonic variants are in the variant_function while the exonic_variant_function is empty. (#97)

use table_annovar. This is NOT a vcf file, and you should never treat it as a VCF file. Read quick startup guide thoroughly and read the website thoroughly.

On Thu, Jun 25, 2020 at 10:46 AM Jiny000 <notifications@github.com> wrote:

> Hi, > I used annovar with below command to annotate the result of pbsv: > > /share/home/annovar/convert2annovar.pl -format vcf4 sample.vcf >sample.annovar > > /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE > > > intergenic TraesCS1D02G001600(dist=16666),TraesCS1D02G001700(dist=12310) chr1D 434819 434819 A 0 het . 30 > > intergenic TraesCS1D02G001600(dist=26665),TraesCS1D02G001700(dist=2311) chr1D 444818 444818 T 0 het . 28 > > exonic TraesCS1D02G001700 chr1D 448395 448395 T 0 het . 15 > > intergenic TraesCS1D02G002200(dist=13802),TraesCS1D02G002300(dist=19271) chr1D 528898 528898 G 0 het . 9 > > intergenic TraesCS1D02G002200(dist=14929),TraesCS1D02G002300(dist=18144) chr1D 530025 530025 T 0 het . 5 > > intergenic TraesCS1D02G002200(dist=21479),TraesCS1D02G002300(dist=11594) chr1D 536575 536575 T 0 het . 21 > > …… > > > It is clear that there are exonic variant in the sample.variant_function > file.However,the related sample.exonic_variant_function file is empty.Why? > The annovar input file is below: > > chr1D 33198 33198 G 0 het . 6 > > chr1D 33210 33210 T 0 het . 8 > > chr1D 33952 33952 T 0 het . 5 > > chr1D 77394 77394 C 0 het . 14 > > chr1D 291865 291865 A 0 het . 17 > > chr1D 291881 291881 C 0 het . 23 > > …… > > > I have tried use awk '$3=$3+1,OFS="\t"' sample.annovar and awk > '$3=$3+1,OFS="\t"' sample.annovar |awk '$5="T",OFS="\t"' |awk > '$4="A",OFS="\t"' to generate different fake annovar files.But all of > sites in them are attributed to invalid_input.I wonder if it is a bug or it > is due to the input file wrong I used. > Here is the log file: > > ANNOVAR Version: > > $Date: 2018-04-16 00:43:31 -0400 (Mon, 16 Apr 2018) $ > > ANNOVAR Information: > > For questions, comments, documentation, bug reports and program update, please visit http://www.openbioinformatics.org/annovar/ > > ANNOVAR Command: > > /share/home/annovar/annotate_variation.pl --geneanno --buildver SAMPLE --outfile sample sample.annovar /share/home/SAMPLE > > ANNOVAR Started: > > Thu Jun 25 21:37:48 2020 > > NOTICE: Output files were written to sample.variant_function, sample.exonic_variant_function > > NOTICE: Reading gene annotation from /share/home/SAMPLE/SAMPLE_refGene.txt ... Done with 298774 transcripts (including 0 without coding sequence annotation) for 269428 unique genes > > NOTICE: Processing next batch with 109504 unique variants in 109504 input lines > > > > > Sincerely, > Jingyao > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <https://github.com/WGLab/doc-ANNOVAR/issues/97&gt;, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/ABNG3OHI7BO2UGLD5EWAT3LRYNPOFANCNFSM4OIOGEOA&gt;

> . >

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