Read color code

[p-levy]

Hi Kez,
I'm seeing some funky color reads in a sample when using gw that I don't when using IGV. Do you have any idea what's the reason? Is there a way to know the color/shade code?
Thanks!

[kcleal]

Hi @p-levy,
I think the grey shaded bases could be N bases in the reads. It looks like GW has soft-clips turned on, but IGV does not?
This could be a bug in GW also. If you could send me this region as a bam file, I could take a look.

[p-levy]

Great for you! Have a nice Xmas break!

[p-levy]

Hi Kez, did you manage to have a look at this? Happy new year!

[kcleal]

Hi @p-levy,
Sorry I have not had a chance. I will take a look tomorrow, sorry about the delay.

[kcleal]

Hi @p-levy,

That should be fixed now - there was incorrect handling of the CREF_SKIP cigar operation. You will need to build gw from source whilst the next release is prepared - the next release will take a week or two.

[p-levy]

Thanks! I'll test it asap.