Sam Format Optional Fields Specification
Hey there,
I currently try to find out what the flag XA:Z: means. I looked through this PDF optional field specification but it just says that tags starting with X are reserved for end users. So does anyone know what this flag means? Here is one example of my sam file. This is a result of a mapping against a multi fasta reference.
M_K00149:52:HJKW7BBXX:4:2126:5720:40913 16 AB032433_chimp_gorilla 18 0 88M * 0 0 AAACTCTGCAAGATCCCAGAGTGAGGGGCCTGTATTTTCCTGCTGGTGGCTCCAGTTCAGGAACAGTAAACCCTGTTCCGAATACTGC A<FFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA RG:Z:IL235-Kars_537_M.NA.NA.170524_K00149_0052_BHJKW7BBXX.G05692 XT:A:R NM:i:5 X0:i:3 X1:i:0 XM:i:5 XO:i:0 XG:i:0 MD:Z:2G7G11A42T1G20 XA:Z:gibbon_orang_1_restored,-18,88M,5;D,-20,88M,5;
I aligned Shotgun data with bwa aln against the reference. Thanks in Advance :)
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Devon Ryan
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j_susat •
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1 answer
According to the bwa documentation (scroll down a ways), XA tags are Alternative hits; format: (chr,pos,CIGAR,NM;). The Negative position means that it aligns reverse-complemented.
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May depend on the tool used for alignment, what was used? Please be as complete as possible when asking questions.
Sorry. I will add the information.
if you're using bwa, your version is too old, this XA tag was removed in 0.7.5 https://github.com/lh3/bwa/blob/master/NEWS.md#release-075-29-may-2013
maybe It still services(?) XA tags for alternative alignment, and it is different from chimeric alignment which is provided by SA tags