Coloured reads and SNVs

[Nirmal]

Hi there,

I'm looking for mosaic SNVs between 'normal' and 'tumour' samples, and using IGV for manual inspection before validating candidate discordant variants with a SNP assay.

Sometimes I see a clear region, with good coverage and apparent mosaicism in a sample. However sometimes there are coloured reads in the region, and I don't know if that casts doubt over the candidate variant. I'm told that coloured reads can show insertions, deletions, and some some may show that a particular read may also map elsewhere.

In short, can I trust a somatic variant that's overlapping a coloured read?

Thank you for your help!
Nirmal

[James Robinson]

Hi, we can help you with interpreting the colors, but not with drawing conclusions.   See http://software.broadinstitute.org/software/igv/AlignmentData  for an explanation of the various colors.   WRT your other question you might post a question to analysis oriented boards, or biostar.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/a5192ce4-0a97-4118-b55c-660260d84a4f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Nirmal]

Thank you for your prompt reply!

I read about the different coloured reads, but find it a little confusing. I sort of understand the coloured reads in the context of an insertion or inversion etc, but when one is overlapping a variant, I don't know if it means that the region also maps elsewhere. If so, it may indicate a false positive.

What default colour indicates that the read maps elsewhere?

This is an example of what I see, but I can't seem to find an answer to my question: http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/igv_aligncenter.jpg

Please send me a link to a messaging board that may address my question, if it's not appropriate here.

Thanks again,
Nirmal

On Tuesday, 25 July 2017 21:29:02 UTC+1, Jim Robinson wrote:

Hi, we can help you with interpreting the colors, but not with drawing conclusions.   See http://software.broadinstitute.org/software/igv/AlignmentData  for an explanation of the various colors.   WRT your other question you might post a question to analysis oriented boards, or biostar.

On Tue, Jul 25, 2017 at 1:22 PM, Nirmal <nirmaldil...@gmail.com> wrote:

Hi there,

I'm looking for mosaic SNVs between 'normal' and 'tumour' samples, and using IGV for manual inspection before validating candidate discordant variants with a SNP assay.

Sometimes I see a clear region, with good coverage and apparent mosaicism in a sample. However sometimes there are coloured reads in the region, and I don't know if that casts doubt over the candidate variant. I'm told that coloured reads can show insertions, deletions, and some some may show that a particular read may also map elsewhere.

In short, can I trust a somatic variant that's overlapping a coloured read?

Thank you for your help!
Nirmal

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[James Robinson]

There is no color for "read maps elsewhere".   If the aligner assigns a mapping quality of zero the read will have a high alpha transparency (appear "hollow") with a solid outline.   Mapping quality of zero is a convention some aligners use to indicate an ambiguous mapping.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/182a54a3-2094-4e14-a38a-55c32b82aeb4%40googlegroups.com.