Black color reads in IGV: bwa-meth

Question

[mehran.karimzade]

Using bwa-meth for whole genome bisulfite sequencing, I found that reads are shown in black.

Same file analyzed by Bismark, has grey colour reads az expected.

Example of reads:

BWA-meth file Ex_1:

HWI-ST762:353:C5PD6ACXX:7:2202:10147:48446      163     chr1    10005   12      99M     =       10092   145     CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT     BBBFFFFFFFFFFF<BFFFIBFFFBFFFIFIFBFFFIFFIIFFBFFIIIBFFFFFI'7<BFF7BFFFFBBBBBB0<BBBB0777BBBB7BBBBBBBBBB  YC:Z:GA MD:Z:99 YD:Z:r  PG:Z:MarkDuplicates     RG:Z:HI.2280.007.Index_3.SE_pair_val_   NM:i:0  AS:i:99 XS:i:99

Bismark-bowtie2 Ex_2:

HWI-ST762:353:C5PD6ACXX:4:2102:15861:95520/1    163     chr1    10005   42      99M     =       10059   105     CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCT     BBBFFFFFFFBFBFFFFIIFBFFFIIIF<FBFFFIFFFBFBBFFFFFFFIIBF<FB<<BF0B'77BBF<77<BB<BBBBB<B<7<<77B7<B7BBB7B<  MD:Z:99 PG:Z:MarkDuplicates.2   XG:Z:GA NM:i:0  XM:Z:...................................................................................................    XR:Z:GA

The only difference I noticed is the fact that pair information is not available in bwa-meth output. However as you see in the screenshot, IGV is able to find reads. I would appreciate any input on what might be the reason.

Many thanks

Mehran

[Devon Ryan]

The pairing information is there in both, but the methylation call string isn't there for bwa-meth (it doesn't produce it). Perhaps that's the reason IGV is treating the alignments differently.

[mehran.karimzade]

You are right. I got this from Jim Robinson IGV mailing list:

This is caused by the "YC" tag, which igv interprets as an explicit color setting. This is a common use of this tag, not in the spec as Y is user-defined but a common long-standing convention that IGV supports. In this case it tries to convert "GA" to a color and fails so black is used."

Thanks

[brentp]

good to know

[14134125465346445]

Is the YC tag used by other tools downstream? Can it be changed to another tag with no consequences?