Viewing RNA-seq data by IGV, I found that position of some indels shifts bases.

[Jingxin Fu]

Hi, I am trying to view variants, called based on the reference genome, from RNA-seq data by IGV. 

For example:

According to the annotation file of variants, the INS should occur at the position where the dash line around. However, the INS indicated from IGV(I) occurs at the position where the red box around. 

So, i am confused about the result. Could anyone explain this to me? Thanks!

[James Robinson]

IGV is just showing you what is in the BAM file, it does not do any interpretation.    If you want me to take a closer look right-click and select "Export alignments" near the bottom of the menu.   Save the file and attach it here.

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[Jingxin Fu]

Thanks for your reply. I have attached the file here. Please take a closer look.

在 2017年1月11日星期三 UTC+8上午1:49:31，Jim Robinson写道：

IGV is just showing you what is in the BAM file, it does not do any interpretation.    If you want me to take a closer look right-click and select "Export alignments" near the bottom of the menu.   Save the file and attach it here.

On Tue, Jan 10, 2017 at 6:14 AM, Jingxin Fu <jingxi...@gmail.com> wrote:

Hi, I am trying to view variants, called based on the reference genome, from RNA-seq data by IGV. 

For example:

According to the annotation file of variants, the INS should occur at the position where the dash line around. However, the INS indicated from IGV(I) occurs at the position where the red box around. 

So, i am confused about the result. Could anyone explain this to me? Thanks!

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[James Robinson]

Hi,  yes IGV is showing exactly what is in the BAM file.   I'm not really sure what your question is.    As you can see from the alignments there is what looks to be a hemizygous insertion between positions 370088,139 and 37,008,140.    That's all I can tell you.   If you have questions about other data files you should ask the source of those files.

Jim

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[Jingxin Fu]

Thanks for your explanation!

在 2017年1月12日星期四 UTC+8下午2:59:20，Jim Robinson写道：

Hi,  yes IGV is showing exactly what is in the BAM file.   I'm not really sure what your question is.    As you can see from the alignments there is what looks to be a hemizygous insertion between positions 370088,139 and 37,008,140.    That's all I can tell you.   If you have questions about other data files you should ask the source of those files.

Jim

On Wed, Jan 11, 2017 at 10:14 PM, Jingxin Fu <jingxi...@gmail.com> wrote:

Thanks for your reply. I have attached the file here. Please take a closer look.

在 2017年1月11日星期三 UTC+8上午1:49:31，Jim Robinson写道：

IGV is just showing you what is in the BAM file, it does not do any interpretation.    If you want me to take a closer look right-click and select "Export alignments" near the bottom of the menu.   Save the file and attach it here.

On Tue, Jan 10, 2017 at 6:14 AM, Jingxin Fu <jingxi...@gmail.com> wrote:

Hi, I am trying to view variants, called based on the reference genome, from RNA-seq data by IGV. 

For example:

According to the annotation file of variants, the INS should occur at the position where the dash line around. However, the INS indicated from IGV(I) occurs at the position where the red box around. 

So, i am confused about the result. Could anyone explain this to me? Thanks!

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