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  • I see, but what it their DP? it cannt be DP=0 (As written in the info field) ...?
  • Hi Sheila, i am using 3.1.1. version of GATK, and i have not used VQSR filtering in this project. where did you see the AD values? there were not omitted in the VCF records. . without getting too much into the details of GATK algorithm, can yo…
  • Hi i re-run the HaplotypeCaller again in the intervals of the 2 examples listed above with the bamout argument. these are the IGV screenshots i got from thr bamout file Hope it will help Many thanks Moran
  • Hi Sheila, i still don't understand. shoudl i re-run the Haplotype Caller on the bams with bamout argument? i see that it would cost lots of time and not recommended. did you mean i'll turn te bamout flag on only for those variants? if so, how do …
  • sorry, the first example correspond to this record: chr7 71912741 . TGTACACAC T 99.14 . AC=2;AF=1.00;AN=2;DP=0;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=0.00;MQ0=0 GT:GQ:PL 1/1:10:136,10,0
  • Thanks for your help here are two examples: example 1: chr7 107336463 . C T 457.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.440;ClippingRankSum=0.320;DP=126;FS=0.000;MLEAC=1;MLEAF=0.500;MQ example 2: chr8 2131251 . …
  • thanks for your quick reply! so, what command should i be using? the analysis is only joined at the var call step (i.e, the processing of BAM files - local realignment, variant qaulity recalibration etc.. is done separately?). it should be noted the…
  • does GATK support Ion_Torrent data for teh base quality recalibration process? (i know taht it was asked here before, but i wonder if anything changed since then.) i get this message error: RROR MESSAGE: The platform (ION_TORRENT) associated with r…