In Bowtie2'S Sam Output, What Does The Yt Attribute Mean?

Question

[Eric Fournier]

In Bowtie2's SAM output, what does the YT flag mean? I can't seem to find a mention of it in Bowtie2's documentation, and the SAM specification says that attributes starting with Y are reserved for the software.

Answer 1

[Vikas Bansal]

I am not sure if it is mentioned in documentation but when you download bowtie2, in source code (file - sam.h) all fields are mentioned-

// Following are Bowtie2-specific
    bool print_yf_; // YF:i: Read was filtered out?
    bool print_yi_; // YI:Z: Summary of inputs to MAPQ calculation
    bool print_ym_; // YM:i: Read was repetitive when aligned unpaired?
    bool print_yp_; // YP:i: Read was repetitive when aligned paired?
    bool print_yt_; // YT:Z: String representing alignment type
    bool print_ys_; // YS:i: Score of other mate
    bool print_zs_; // ZS:i: Pseudo-random seed
    bool print_xr_; // XR:Z: Original read string
    bool print_xt_; // XT:i: Time taken to align
    bool print_xd_; // XD:i: DP problems
    bool print_xu_; // XU:i: ungapped alignment
    bool print_ye_; // YE:i: streak of failed DPs at end
    bool print_yl_; // YL:i: longest streak of failed DPs
    bool print_yu_; // YU:i: index of last succeeded DP
    bool print_yr_; // YR:i: # redundant seed hits
    bool print_zf_; // ZF:i: # FM Index ops
    bool print_zi_; // ZI:i: # extend loop iters
    bool print_zp_; // ZP:i: Score of best/second-best paired-end alignment
    bool print_zu_; // ZU:i: Score of best/second-best unpaired alignment

[Eric Fournier]

Thank you! By looking throught he source code, I also found the meaning for the attribute values:

if(alignedConcordant()) {
    o.append("CP");
} else if(alignedDiscordant()) {
    o.append("DP");
} else if(alignedUnpairedMate()) {
    o.append("UP");
} else if(alignedUnpaired()) {
    o.append("UU");
}

[Eric Fournier]

Thank you! By looking through the source code, I also found the meaning for the attribute values: CP: Concordant; DP: Discordant; UP: Unpaired Mate; UU: Unpaired.