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vibansal / crisp

Code for multi-sample variant calling from sequence data of pooled or unpooled DNA samples
MIT License
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output for MLAC tag in vcf #5

Closed bfairkun closed 3 years ago

bfairkun commented 6 years ago

It seems CRISP isn't outputting the MLAC tag for all entries in the vcf.

Here are 3 sample lines from an output vcf. 

MT      2363    .       T       TC      151701  PASS    NP=2;DP=4583,3688,0;VT=INSERTION;CT=-inf;VP=2;VF=EMpass;AC=40;AF=1.00000;EMstats=15170.12:-6776.05;HWEstats=-0.0;MQS=0,0,33,9581;HP=1;FLANKSEQ=actcaaccta:TC:tccggttgta MLAC:GQ:DP:ADf:ADr      20:602:4583:86,2047:78,1785     20:610:5031:114,2336:77,1748    
II      153847  .       C       T       822     LowDepth        NP=2;DP=31,33,0;VT=SNV;CT=nan;VP=2;VF=EMpass;AC=23;AF=0.55953;EMstats=82.24:-40.87;HWEstats=-0.0;MQS=0,0,1,71;FLANKSEQ=aatgaaagct:C:tacacgaaag  MLAC:GQ:DP:ADf:ADr      11:1:40:7,9:9,9 12:0:32:7,8:5,10        
II  858506  .   G   A   696 LowDepth    NP=2;DP=13,26,0;VT=SNV;CT=-inf;VP=1;VF=EMpass;AC=25;AF=0.61958;EMstats=69.65:-18.63;HWEstats=-0.0;MQS=0,0,0,44;FLANKSEQ=aagcgtgctc:G:agactgaaag MLAC:GQ:DP:ADf:ADr  17:0:24:0,7:0,15    .:0:20:6,0:9,2

Notice that for the last entry, last sample (last column) reads

.:0:20:6,0:9,2

so the MLAC tag has a "." where I was expecting an integer. Anyway I can get an integer for all MLAC tags?

Much thanks!