Question about SNV list

[rz2333]

Hi qing,

I'm new to bioinformatics and I'm wondering how other users get the list of SNVs? I'm analyzing data from mouse and I could download dbSNPs information from UCSC. Thanks for your time!

Bests,
Ray

[zhqingit]

Hi Ray,

You can get the list by using GATK or other SNV calling methods.

Best,
Qing

2016-10-03 13:45 GMT-07:00 Rui Hong notifications@github.com:

Hi qing,

I'm new to bioinformatics and I'm wondering how other users get the list
of SNVs? I'm analyzing data from mouse and I could download dbSNPs
information from UCSC. Thanks for your time!

Bests,
Ray

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[zhqingit]

Hi Ray,

GIREMI is designed to find the RNA editing sites from a mixture of the RNA
editing sites and SNPs. I am not clear what's your purpose to input a file
with all SNPs?

Best,
Qing

2016-10-04 10:03 GMT-07:00 Rui Hong notifications@github.com:

Hi Qing,

Thanks for your reply! Could I use dbSNPs information downloaded from
UCSC, format them correctly and take this file as SNV list? In this case,
the column 5 are all 1. Does this work?

Thanks,
Ray

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[rz2333]

Hi Qing,

Sorry, I misunderstood how does GIREMI work. Now I know how to makes it
work. Thanks a lot!

Bests,
Ray

On Wed, Oct 5, 2016 at 2:06 PM, zhqingit notifications@github.com wrote:

Hi Ray,

GIREMI is designed to find the RNA editing sites from a mixture of the RNA
editing sites and SNPs. I am not clear what's your purpose to input a file
with all SNPs?

Best,
Qing

2016-10-04 10:03 GMT-07:00 Rui Hong notifications@github.com:

Hi Qing,

Thanks for your reply! Could I use dbSNPs information downloaded from
UCSC, format them correctly and take this file as SNV list? In this case,
the column 5 are all 1. Does this work?

Thanks,
Ray

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[JohnMCMa]

I'd need to make a reminder, however--given GATK's HaplotypeCaller and MuTect2 tools performs local reassembly for variant calling, I think it'd be safer to use the tools' bamout as the bam input for GIREMI.