search

WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
225 stars 347 forks source link

Indel classification conversion #143

Open faraz89 opened 3 years ago

faraz89 commented 3 years ago

Hi, I have used the tool to annotate and filter variants. My question is how to replace the "_" (hyphen) to the actual bases in a avinput vcf for indels from annovar converted file.

I have already got the sequence from retrieve_seq_from_fasta.pl, but I am confused how to now transfer these sequences back the vcf file. Would you be able to provide some guidance on this? Many thanks.

Best Wishes, Faraz.

kaichop commented 3 years ago

Generally speaking, you should use VCF file directly as input, and then you will get the VCF file with the same record in the output file. Do not do any conversion yourself since your goal is to use the original VCF records.

On Thu, May 27, 2021 at 3:52 AM Faraz Khan @.***> wrote:

Hi, I have used the tool to annotate and filter variants. My question is how to replace the "_" (hyphen) to the actual bases in a avinput vcf for indels from annovar converted file.

I have already got the sequence from retrieve_seq_from_fasta.pl, but I am confused how to now transfer these sequences back the vcf file. Would you be able to provide some guidance on this? Many thanks.

Best Wishes, Faraz.

— 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/143, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OFSMQ75LYVASOECV4DTPX227ANCNFSM45TVTCSQ .

faraz89 commented 3 years ago

Thank you for the input. However, as my purpose is to filter variants present in various databases (eg. 1000g2015aug_all, esp6500siv2_all), I have no choice but to convert the vcf to annovar format as "annotate_variation.pl " does not work on "vcf" file.

Or is it possible to use vcf for "annotate_variation.pl" If I am not aware. Please let me know. Many thanks @kaichop

kaichop commented 3 years ago

This is a standard task in ANNOVAR. You should use table_annovar.pl that can do all these things that you just mentioned in one command on a VCF file. Read quick start-up guide.

On Thu, May 27, 2021 at 10:54 AM Faraz Khan @.***> wrote:

Thank you for the input. However, as my purpose is to filter variants present in various databases (eg. avSNP, ESP), I have no choice but to convert the vcf to annovar format as "annotate_variation.pl " does not work on "vcf" file.

Or is it possible to use vcf for "annotate_variation.pl" If I am not aware. Please let me know. Many thanks.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/143#issuecomment-849702637, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCK4IY7BITYPVXLJ5DTPZMJ7ANCNFSM45TVTCSQ .

faraz89 commented 3 years ago

Many thanks! I will certainly do.

Best wishes, Faraz

faraz89 commented 3 years ago

I just had a look but I don't see the options I need in table_annovar.pl.

For example, I need to use "filter" and "dbtype" arguments to remove variants that have maf > 0.01 in "1000g2015aug_all but I can't do that using "table_annovar.pl".

Do I need to pipe directly from table_annovar.pl to annotate_variation.pl? If yes, can you please send a quick example code @kaichop

kaichop commented 3 years ago

table_annovar is for annotation. If you need to remove variants based on a set of criteria, you can write a script to do that after generating the output file.

On Thu, May 27, 2021 at 11:55 AM Faraz Khan @.***> wrote:

I just had a look but I don't see the options I need in table_annovar.pl.

For example, I need to use "filter" and "dbtype" arguments to remove variants that have maf > 0.01 in "1000g2015aug_all but I can't do that using "table_annovar.pl".

Do I need to pipe directly from table_annovar.pl to annotate_variation.pl? If yes, can you please send a quick example code @kaichop https://github.com/kaichop

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/WGLab/doc-ANNOVAR/issues/143#issuecomment-849748412, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OEZAJWFZFJWRW4R6DDTPZTNPANCNFSM45TVTCSQ .