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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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Empty genotype GT for some indels ? #57

Closed tseemann closed 4 years ago

tseemann commented 4 years ago 
ctg001  282576  .       TT      T       95      PASS    RC=0;TYPE=del   GT:GQ:DP:AD:AF:F1R2:F2R1        1:95:60:22,38:0.63:19,20:1,0
ctg001  318519  .       T       TT      100     PASS    RC=0;TYPE=ins   GT:GQ:DP:AD:AF:F1R2:F2R1        1:100:6:0,6:1.00:3,0:1,2
ctg001  455183  .       T       TT      54      PASS    RC=0;TYPE=ins   GT:GQ:DP:AD:AF:F1R2:F2R1        :54:6:0,6:1.00:6,0:5,0

The GT is empty on the last variant?

MapCaller 0.9.9.35
-ploidy 1 -maxmm 0.03 -ad 20

Why is it reporting indels with DP/AD < 20 when i have -ad 20 ?

hsinnan75 commented 4 years ago

Thanks for reporting this bug. I'll look into it.

hsinnan75 commented 4 years ago

I used another parameter to be the threshold of indel event. Now it is the same as ad. Please update your MapCaller and test again. Thank you!

tseemann commented 4 years ago

Seems to be fixed