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What Are The Next Steps For Processing Indels From Gatk

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Hi, I have raw calls for indels called using GATK, I wonder, where to start? filtering these calls? Should I plot the quality, depth etc. and then decide threshold to filter the bad calls? Any suggestions, scripts would be useful.

chr10    264423    .    G    GC    29875    .    AC=26;AF=1.00;AN=26;BaseQRankSum=-0.054;DP=717;FS=8.633;HaplotypeScore=344.1280;InbreedingCoeff=-0.0046;MLEAC=26;MLEAF=1.00;MQ=38.57;MQ0=0;MQRankSum=-0.832;QD=41.67;RPA=1,2;RU=C;ReadPosRankSum=0.979;SB=-4.035e+03;STR    GT:AD:DP:GQ:PL    1/1:6,242:250:99:10448,743,0    1/1:10,193:203:99:8479,571,0    1/1:3,142:148:99:6167,439,0    1/1:0,13:13:39:551,39,0    1/1:1,9:10:30:424,30,0    1/1:1,13:15:39:550,39,0    1/1:0,9:9:27:382,27,0    1/1:1,15:16:48:667,48,0    1/1:1,11:12:33:467,33,0    1/1:1,8:9:27:382,27,0    1/1:0,18:18:54:764,54,0    1/1:0,11:11:33:467,33,0    1/1:0,3:3:9:127,9,0

Looking forward for your suggestions and feedback. /Bari,


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