(Copied) IGV problem: How to turn off the mismatch or SNP color on coverage view
How to turn off the mismatch or SNP color on coverage view
I would like to learn how to turn off the mismatch or SNP colors that showed on the coverage view.( have attached an image to show what I meant with this message) I tired to change the setting in the "Preference"and the "Color Legends" but it did not work.
Could any one who know how to do it provide any advice to me? Many thanks in advanced!!
Could any one who know how to do it provide any advice to me? Many thanks in advanced!!
Answer:
You can right click on the coverage track, select "Set allele frequency threshold..." and set it to 1.0.
This sets the highest threshold of when to display the colored bar, and you should only see them where 100% of the reads are high-quality mismatches.
You can also compute the read coverage from the bam file (using the igvtools count command) and load the resulting file explicitly as a separate track. The separate track will not show any mismatches.
Helga
This sets the highest threshold of when to display the colored bar, and you should only see them where 100% of the reads are high-quality mismatches.
You can also compute the read coverage from the bam file (using the igvtools count command) and load the resulting file explicitly as a separate track. The separate track will not show any mismatches.
Helga
References:
https://groups.google.com/forum/#!topic/igv-help/aukP9W765jA
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