Wei Zhu

Many thanks for your rapid reply. Best, -Wei From: Brent Pedersen Reply-To: brentp/goleft Date: Friday, July 19, 2019 at 10:59 AM To: brentp/goleft Cc: Wei Zhu , Author Subject: Re:...

Riccardo; Thank you for the reply, which is very helpful. Actually, I had figured out to use the solution two, following the Rstudio example. Nevertheless, your reply makes me more...

I have a similar issue: FILTER="LowPratio", PASS_AC=0, but many samples have FT of "PASS" 10616 1:10616:DG N 20124 LowPratio ABHet=-1;ABHetMulti=-1,-1;ABHom=0.9903;ABHomMulti=-1,0.9903;AC=160;AF=1;AN=160;CR=0;CRal=0,0;CRalt=0;END=10753;MMal=0,99;MMalt=0.0034555;MQ=4;MQSal=0,50860;MQalt=4;MQsquared=50860;MaxAAS=70;MaxAASR=1;MaxAltPP=0;NHet=0;NHomAlt=80;NHomRef=0;NUM_MERGED_SVS=1;PASS_AC=0;PASS_AN=0;PASS_ratio=0;QD=24.71;QDalt=24.71;RefLen=1;SB=0.2353;SBAlt=0.2353;SBF=0,4;SBF1=0,4;SBF2=0,0;SBR=0,13;SBR1=0,11;SBR2=0,2;SDal=0,407;SDalt=0.142059;SVLEN=137;SVMODEL=AGGREGATED;SVSIZE=137;SVTYPE=DEL;SV_ID=1;SeqDepth=2893;VarType=DG GT:FT:AD:MD:DP:RA:PP:GQ:PL 1/1:PASS:0,30:0:30:0,0:0:90:255,90,0 1/1:PASS:0,42:0:42:0,0:0:99:255,126,0 1/1:PASS:0,34:0:34:0,0:0:99:255,102,0 1/1:PASS:0,43:0:43:0,0:0:99:255,129,0 1/1:PASS:0,39:0:39:0,0:0:99:255,117,0 1/1:PASS:0,35:0:35:0,0:0:99:255,105,0 1/1:PASS:0,31:0:31:0,0:0:93:255,93,0 1/1:PASS:1,46:0:47:0,0:0:99:255,129,0 1/1:PASS:0,43:0:43:0,0:0:99:255,129,0...