MSI/MSS evaluation by using lobSTR

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newton...@gmail.com

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Aug 10, 2017, 12:00:27 AM8/10/17

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Hi guys

we are now using lobstr for MSI status detection for human NGS data generated from illumina X10 platform. And we are concerned with the allelotype in certain number of mononucleotide STR makers we designed in our panel, such as : MONO-27, BAT-26 and so on .

I just checked the vcf output from one sample, for the marker MONO-27, it reported like below:

> chr2 39536690 . TTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTT,TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 9.99964e+06 . END=39536716;MOTIF=T;NS=1;REF=27;RL=27;RU=T;VT=STR;RPA=29,31 GT:ALLREADS:AML:DISTENDS:DP:DPA:GB:PL:PQ:Q:SB:STITCH 1/2:-1|1;0|5;1|7;2|9;3|4;4|1;7|1:0.991178/0.996765:47.7:28:106:2/4:9640,9640,9640,76,0,9640:1.91875:0.987943:26:0

but for the other markers like BAT-26, it reported like this:

> chr2 47641560 . AAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAA 0 . END=47641586;MOTIF=A;NS=1;REF=27;RL=27;RU=A;VT=STR;RPA=-9973 GT:ALLREADS:AML:DISTENDS:DP:DPA:GB:PL:PQ:Q:SB:STITCH 1/1:-10|2;-9|1;-8|4;-7|1;-6|8;-5|10;-4|16;-3|13;-2|28;-1|20;0|9;1|1;6|1:-nan/-nan:0:114:245:-10000/-10000:-9990000,-10000000,-10000000:nan:-nan:2:0

So is there any tags which could provide us the information about whether this STR marker is stable or unstable? Because as I understand, if it gave a confirmed called status such as the upper report (RPA=29,31 vs ref is 27), then it should be a stable marker in this sample; otherwise it is an unstable marker like the lower report (RPA=-9973 vs ref=27). Am I correct? or some other tags could provide the information?