annovar output - the meaning of REJECT?

dkrtndhkd · 08-03-2012, 09:58 PM

Hi,

I want to know the meaning of 'REJECT' of output file of ANNOVAR like follow:

line2 nonsynonymous SNV MLH1:NM_001167619:exon11:c.T428A

.V143D,MLH1:NM_001167618:exon12:c.T428A

.V143D,MLH1:NM_000249:exon12:c.T1151A

.V384D,MLH1:NM_001167617:exon12:c.T857A

.V286D, 3 37067240 37067240 T A tissue blood 0 DBSNP UNCOVERED 0 0.120436 0 0 0 0 9.276976 0.363636 0.02 -0.096427 7 4 181 105 0 0 AT -20.427446 3 7 84 201 REJECT

Thank you!

Heisman · 08-04-2012, 10:23 PM

ANNOVAR keeps all of the input columns and puts them at the end of the annotation columns. "REJECT' was in the input file.

shyam_la · 08-06-2012, 12:42 AM

It appears you have used MuTect to call your SNVs. The current beta version of MuTect is very verbose and the initial output is more than a hundred fold bigger than it should be.

use "grep -v REJECT variant_file > variant_file_KEEP" to get the real variants and then annotate.
You may also want to remove "UNCOVERED" variants and "DBSNP" variants.. The example variant you have given is a total failure..

dkrtndhkd · 08-14-2012, 11:13 AM

Thank you!!!!

I see it now because the alarm mail was in spam box...

another question!

is there any option of MuTect to get output with VCF format???

shyam_la · 08-14-2012, 05:15 PM

No, not currently, as far as I know.. May I ask why you specifically want it in vcf format?

dkrtndhkd · 08-14-2012, 07:36 PM

because in my pipeline, i use ANNOVAR tool for annotation step and ANNOVAR gets input file with VCF format

I know I can change some column to make input file(vcf4.0 format) for ANNOVAR,

but I also want to bring other info as i wrote above.

however, after changing the form of MuTect result file to vcf4.0 file, the ANNOVAR result file is not uniform according to each line of MuTect result file, so it's hard to see it.

it's the reason

Heisman · 08-18-2012, 11:50 AM

The annovar input file only needs 5 columns; you can check the website to see the proper format (it's chr/base/base/ref/var for SNPs, check for indels and make sure it makes sense to you). Once you figure that out it should be easy to take your variant files and add 5 initial columns with the correct information; the rest will carry through so you won't lose anything.

jp. · 03-25-2014, 01:59 AM

I tried using MuTect output .bam.out to convert into avinput, however, the format was not proper and I got no annotations after annovar. Moreover, when I used sed '/REJCT/d' input.bam.out > output_file ; it worked and there was no problem. But I want to include 'REJCT' also and filter it out later after annovar is done. Is there something wrong with my commands. The same commands worked after removing 'REJCT' but not working with 'REJECT'.
My commands are:
$ perl ./annovar/convert2annovar.pl -format vcf4 call_status.bam.out > call_status.bam.avinput

$ perl ./annovar/annotate_variation.pl --geneanno call_status.bam.avinput ./annovar/humandb --buildver hg19

$ perl ./annovar/summarize_annovar.pl call_status.bam.avinput ./annovar/humandb/ --buildver hg19 --verdbsnp 137 --ver1000g 1000g2012apr --veresp 6500 --genetype refgene --outfile annovar_snp_annotated.txt --remove
Can somebody tell something ?
thank you in advance.

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08-03-2012, 09:58 PM	#1
dkrtndhkd Member Location: Seoul Join Date: Jan 2012 Posts: 42	annovar output - the meaning of REJECT? Hi, I want to know the meaning of 'REJECT' of output file of ANNOVAR like follow: line2 nonsynonymous SNV MLH1:NM_001167619:exon11:c.T428A.V143D,MLH1:NM_001167618:exon12:c.T428A.V143D,MLH1:NM_000249:exon12:c.T1151A.V384D,MLH1:NM_001167617:exon12:c.T857A.V286D, 3 37067240 37067240 T A tissue blood 0 DBSNP UNCOVERED 0 0.120436 0 0 0 0 9.276976 0.363636 0.02 -0.096427 7 4 181 105 0 0 AT -20.427446 3 7 84 201 REJECT Thank you!

08-14-2012, 11:13 AM	#4
dkrtndhkd Member Location: Seoul Join Date: Jan 2012 Posts: 42	thank you Thank you!!!! I see it now because the alarm mail was in spam box... another question! is there any option of MuTect to get output with VCF format???

08-04-2012, 10:23 PM	#2
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	ANNOVAR keeps all of the input columns and puts them at the end of the annotation columns. "REJECT' was in the input file.

08-06-2012, 12:42 AM	#3
shyam_la Member Location: California Join Date: Mar 2012 Posts: 97	It appears you have used MuTect to call your SNVs. The current beta version of MuTect is very verbose and the initial output is more than a hundred fold bigger than it should be. use "grep -v REJECT variant_file > variant_file_KEEP" to get the real variants and then annotate. You may also want to remove "UNCOVERED" variants and "DBSNP" variants.. The example variant you have given is a total failure..

08-14-2012, 05:15 PM	#5
shyam_la Member Location: California Join Date: Mar 2012 Posts: 97	No, not currently, as far as I know.. May I ask why you specifically want it in vcf format?

08-14-2012, 07:36 PM	#6
dkrtndhkd Member Location: Seoul Join Date: Jan 2012 Posts: 42	because in my pipeline, i use ANNOVAR tool for annotation step and ANNOVAR gets input file with VCF format I know I can change some column to make input file(vcf4.0 format) for ANNOVAR, but I also want to bring other info as i wrote above. however, after changing the form of MuTect result file to vcf4.0 file, the ANNOVAR result file is not uniform according to each line of MuTect result file, so it's hard to see it. it's the reason

08-18-2012, 11:50 AM	#7
Heisman Senior Member Location: St. Louis Join Date: Dec 2010 Posts: 535	The annovar input file only needs 5 columns; you can check the website to see the proper format (it's chr/base/base/ref/var for SNPs, check for indels and make sure it makes sense to you). Once you figure that out it should be easy to take your variant files and add 5 initial columns with the correct information; the rest will carry through so you won't lose anything.

03-25-2014, 01:59 AM	#8
jp. Senior Member Location: NikoNarita.jp Join Date: Jul 2013 Posts: 142	I tried using MuTect output .bam.out to convert into avinput, however, the format was not proper and I got no annotations after annovar. Moreover, when I used sed '/REJCT/d' input.bam.out > output_file ; it worked and there was no problem. But I want to include 'REJCT' also and filter it out later after annovar is done. Is there something wrong with my commands. The same commands worked after removing 'REJCT' but not working with 'REJECT'. My commands are: $ perl ./annovar/convert2annovar.pl -format vcf4 call_status.bam.out > call_status.bam.avinput $ perl ./annovar/annotate_variation.pl --geneanno call_status.bam.avinput ./annovar/humandb --buildver hg19 $ perl ./annovar/summarize_annovar.pl call_status.bam.avinput ./annovar/humandb/ --buildver hg19 --verdbsnp 137 --ver1000g 1000g2012apr --veresp 6500 --genetype refgene --outfile annovar_snp_annotated.txt --remove Can somebody tell something ? thank you in advance.