Allow Allele frequency threshold == 0 or color coverage bar if adjacent tracks show variation

[mmokrejs]

Hi Jim,
it would be helpful to colorize coverage tracks (normally they are gray for BAM files without adjacent VCF file).

I show picture what is colored when Allele frequency threshold is set to 0.0000000000009. I just cannot set it to zero which is pity. :(

For raw inspection of BAM aligned against a reference it would be helpful to see in color all positions for which adjacent tracks have a variation (so not even relying on Allele frequency threshold == 0) but inferring the affected columns from adjacent tracks.

I see the Allele frequency threshold is a globally set value, what would be needed first is to have it per track individually.
Thank you

[jrobinso]

OK, noted, but just a correction. VCF files have no affect on coloring of BAM files.

…

On Wed, Apr 12, 2017 at 7:04 AM, Martin Mokrejš ***@***.***> wrote: Hi Jim, it would be helpful to colorize coverage tracks (normally they are gray for BAM files without adjacent VCF file). [image: igv_feature_request__color_coverage_track_in_100perc_homozygotes] <https://cloud.githubusercontent.com/assets/3297852/24954576/3b80a73c-1f80-11e7-92fe-5d04ef5af9ca.png> I show picture what is colored when Allele frequency is set to 0.0000000000009. I just cannot set it to zero which is pity. :( [image: igv_feature_request__color_coverage_track_in_100perc_homozygotes__allele_freq_threshold] <https://cloud.githubusercontent.com/assets/3297852/24954586/4b52f566-1f80-11e7-90c6-2ce4c5992d09.png> For raw inspection of BAM aligned against a reference it would be helpful to see in color all positions for which adjacent tracks have a variation (so not relying on "Allele frequency threshold == 0") ut inferring the affected columns from adjacent tracks. [image: igv_feature_request__color_coverage_track_in_100perc_homozygotes__actual_allele_freq] <https://cloud.githubusercontent.com/assets/3297852/24954592/5562e958-1f80-11e7-9480-a2dce0d64d0c.png> Thank you — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#388>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AA49HIeORbVHm9JJg0OOlE_ntJFiTvr9ks5rvK_DgaJpZM4M7Rhi> .