XS tag in SAM file

Question

[oghzzang]

Dear users,

Hi. I'm oh.

I have questions about pre-processed bam by GATK4 pipeline (https://github.com/gatk-workflows/gatk4-data-processing/blob/master/processing-for-variant-discovery-gatk4.wdl).

In these processes, they only recommended "--ATTRIBUTES_TO_RETAIN X0" in MergeBamAlignment step.

So, my final recalibrated bam, there is no "XS" tag as follows.

A00126:66:HGLWFDSXX:3:1423:31693:6621   177     chr1    9996    0       93S58M  chr4    190122941       0       CCCCCCCCCCCCCCCCCCCCCCACAAACACCCCCCCCCCCCCCCCCCCCCAAACCCCCCCGCGCCTGTACACTCTTTCCCTACACGACGCTCTTCCGATATCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC ??????????????+??+++++++++++++??+++?????+???+++?+?++++????+???5???+5+??+'???????5????++%5????'?????+'?????????????????????????????????????????????????? MC:Z:100S51M    MD:Z:0N0N0N0N0N2A50     PG:Z:MarkDuplicates     RG:Z:SA00719        NM:i:6  MQ:i:0  UQ:i:158        AS:i:53

In this point, I have two questions.

1. I don't know the meaning of XS tag.

2. How does it affect the post-steps (ex. variant calling, HLA typing, SV detect etc.) when there is no XS tag?

[h.mon]

The X* tags are called locally-defined tags, they optional and reserved to aligner-specific implementations, thus are not part of the SAM specifications:

2 Locally-defined tags

You can freely add new tags. Note that tags starting with ‘X’, ‘Y’, or ‘Z’ and tags containing lowercase letters in either position are reserved for local use and will not be formally defined in any future version of this specification.

I think XS:i and XS:A are bowtie / tophat tags. See some discussions:

AS:i and XS:i SAM File Fields (Bowtie2)

A new SAM tag for transcript strand