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Old 07-15-2015, 06:54 AM   #6
trotos
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Location: Cologne,Germany

Join Date: May 2012
Posts: 12
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Quote:
Originally Posted by Kennels View Post
The "SA" tag is now used (v0.7.5) to identify reads which have chimeric alignment:
https://github.com/lh3/bwa/blob/master/NEWS
hello, I dig up this post because of your comment on the SA: tag
could you please elaborate, the provided link is broken.
the main question is:
are the reads with the SA: code still unique? what about the ones that also incorporate the XA: code?
Here are some examples
Code:
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1102:3525:68438 256     chr2    161581931       0       32M17H  *       0       0       TATCCATTTCATCTGGATTTTCTAGTTTATTT        CAC<E?E<E????DDF@DBEB<D?9??D99D<        NM:i:0  MD:Z:32 AS:i:32 XS:i:20 SA:Z:chr12,87311999,-,32M17S,0,0;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1212:1519:12286 256     chr2    161581931       1       32M19H  *       0       0       TATCCATTTCATCTGGATTTTCTAGTTTATTT        .):639=>?>?8??<)7;7)=8=8)0>8>?.6        NM:i:0  MD:Z:32 AS:i:32 XS:i:27 SA:Z:chr12,87311997,-,34M17S,1,1;       XA:Z:chr12,+46991828,32M19S,1;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:2115:10843:5627 256     chr2    161581931       1       32M19H  *       0       0       TATCCATTTCATCTGGATTTTCTAGTTTATTT        B?@AB@AABBBBABBB<ABBB?BAB?BB?BBB        NM:i:0  MD:Z:32 AS:i:32 XS:i:27 SA:Z:chr12,87311997,-,34M17S,1,1;       XA:Z:chr12,+46991828,32M19S,1;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:2115:14837:88360        256     chr2    161581931       1       32M19H  *       0       0       TATCCATTTCATCTGGATTTTCTAGTTTATTT        B?BBBBBBBB=ABBBBBBB?A?ABB0=A?BBB        NM:i:0  MD:Z:32 AS:i:32 XS:i:27 SA:Z:chr12,87311997,-,34M17S,1,1;       XA:Z:chr12,+46991828,32M19S,1;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1209:6904:71888 0       chr11   22585338        0       18S33M  *       0       0       TTTTCCCATTCTGTAGATTGTCTGTTTACTCTGATTATAGTTTATTTTGCT     IGGIIIIIIIIGA@GGGHFIIIIIFFHEIHIHFGIHIIIIFEIGHEGHCHF     NM:i:0  MD:Z:33 AS:i:33 XS:i:33 SA:Z:chr17,59076122,+,33M18S,0,0;       XA:Z:chr3,+175713108,51M,4;chr2,-116989725,16S35M,1;chr19,+21698327,7S29M15S,0;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1212:1519:12286 16      chr12   87311997        1       34M17S  *       0       0       TCTATAAACACCTCTAAGAAAATAAACTAGAAAATCCAGATGAAATGGATA     ??>?9@?=.:().))?>.)6.?>8>0)8=8=)7;7)<??8?>?>=936:).     NM:i:1  MD:Z:0A33       AS:i:33 XS:i:31 SA:Z:chr2,161581931,+,32M19S,1,0;
       XA:Z:chr9,-104599379,51M,5;chr3,+170653467,51M,5;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:2115:10843:5627 16      chr12   87311997        1       34M17S  *       0       0       TCTATAAACACCTCTAAGAAAATAAACTAGAAAATCCAGATGAAATGGATA     BBBBBBABBABABABBBBBBBB?BB?BAB?BBBA<BBBABBBBAA@BA@?B     NM:i:1  MD:Z:0A33       AS:i:33 XS:i:31 SA:Z:chr2,161581931,+,32M19S,1,0;
       XA:Z:chr9,-104599379,51M,5;chr3,+170653467,51M,5;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:2115:14837:88360        16      chr12   87311997        1       34M17S  *       0       0       TCTATAAACACCTCTAAGAAAATAAACTAGAAAATCCAGATGAAATGGATA     BBBBBBABB>A<B>B>A?7BBB?A=0BBA?A?BBBBBBBA=BBBBBBBB?B     NM:i:1  MD:Z:0A33       AS:i:33 XS:i:31 SA:Z:chr2,161581931,+,32M19S,1,0;       XA:Z:chr9,-104599379,51M,5;chr3,+170653467,51M,5;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1102:3525:68438 16      chr12   87311999        0       32M17S  *       0       0       TATAAACACCTCTAAGAAAATAAACTAGAAAATCCAGATGAAATGGATA       AA==5.DB8BB8=/??*<D99D??9?D<BEBD@FDD????E<E?E<CAC       NM:i:0  MD:Z:32 AS:i:32 XS:i:30 SA:Z:chr2,161581931,+,32M17S,0,0;       XA:Z:chr9,-104599381,49M,4;chr3,+170653467,49M,4;chr12,+46991828,49M,5;
BIOMICS-HISEQHI:522:HCYM5ADXX:2:1209:6904:71888 256     chr17   59076122        0       33M18H  *       0       0       TTTTCCCATTCTGTAGATTGTCTGTTTACTCTG       IGGIIIIIIIIGA@GGGHFIIIIIFFHEIHIHF       NM:i:0  MD:Z:33 AS:i:33 XS:i:32 SA:Z:chr11,22585338,+,18S33M,0,0;       XA:Z:chr4,-151801895,19S32M,0;
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