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VCFtools alternative to --minDP flags not working?

Since my VCFtools --minDP flag and --maxDP are not working, is there a way to manually code the filtering? 

vcftools --vcf output.vcf --recode --recode-INFO-all --minDP 20 --maxDP 25 --out output.reference3

  84681 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  JP3048_for      JP3162_for      JP3171_for      JP3402_for      JP343_for       JP3539_for      JP3
  84682 scaffold440     420     .       T       G       999     .       DP=72;VDB=7.55993e-06;SGB=11.7312;RPB=0.0732065;MQB=0.00151772;MQSB=0.0740741;BQB=0.72433;MQ0F=0;AF1=0.1202
  84683 scaffold440     451     .       C       A       11.216  .       DP=71;VDB=0.0249187;SGB=-0.0412595;RPB=0.910489;MQB=0.70327;BQB=0.638446;MQ0F=0;AF1=0.0946915;AC1=10;DP4=35
  84684 scaffold440     452     .       C       A       10.3236 .       DP=71;VDB=0.02;SGB=-0.018177;RPB=1;MQB=0.162162;BQB=0.986486;MQ0F=0;AF1=0.0848011;AC1=9;DP4=37,0,2,0;MQ=42;
  84685 scaffold440     460     .       A       G       999     .       DP=71;VDB=3.01279e-43;SGB=10.0134;MQSB=0.0392157;MQ0F=0;AF1=1;AC1=112;DP4=0,0,51,2;MQ=43;FQ=-28.9555    GT:
  84686 Scaffold1210    18      .       C       T       17.1031 .       DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84687 Scaffold1210    23      .       A       G       17.1031 .       DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84688 Scaffold1210    30      .       A       G       17.1031 .       DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84689 scaffold420     41      .       T       G       14.1975 .       DP=2;SGB=-0.0045042;MQ0F=0;AF1=1;AC1=112;DP4=0,0,0,1;MQ=44;FQ=-22.7628  GT:PL:DP:SP:GQ  0/1:0,0,0:0:0:3 0/1
  84690 scaffold420     264     .       T       A       85.015  .       DP=4;VDB=0.0162466;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.6007   GT:PL:DP:SP
  84691 scaffold420     265     .       C       A       85.015  .       DP=4;VDB=0.0162466;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.6007   GT:PL:DP:SP
  84692 scaffold420     281     .       A       G       36.0512 .       DP=4;VDB=0.0138351;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.5943   GT:PL:DP:SP
  84693 scaffold420     316     .       G       A       24.3268 .       DP=4;VDB=0.0389723;SGB=-0.0412595;RPB=1;MQB=1;MQSB=0.5;BQB=1;MQ0F=0;AF1=0.749149;AC1=84;DP4=1,0,1,2;MQ=31;F
  84694 scaffold420     465     .       C       T       5.65075 .       DP=3;SGB=-0.0045042;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.333337;AC1=37;DP4=1,1,0,1;MQ=48;FQ=6.99776;PV4=1,
  84695 scaffold420     562     .       A       C       49.0208 .       DP=3;VDB=0.06;SGB=-0.018177;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,0;MQ=43;FQ=-23.6676  GT:PL:DP:SP:GQ  1/1:0,0,0:0
  84696 scaffold420     650     .       C       T       4.15723 .       DP=2;SGB=-0.0045042;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0.5;AF1=1;AC1=112;DP4=1,0,0,1;MQ=24;FQ=-22.0062;PV4=1,1,1
vcf read depth
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updated by igor igor • written by beausoleilmo beausoleilmo

2 answers

GATK SelectVariants might be an alternative.

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written by WouterDeCoster WouterDeCoster

You can also try samtools/bcftools:

bcftools query --include '%DP>20' file.vcf
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written by igor igor

I've tried this, but it wasn't working...

Instead I used this: 

bcftools filter --soft-filter LowQual --exclude 'INFO/DP<100 && %QUAL<20' output.vcf  > output.flts.vcf

But it's doing half of the job (both conditions are met independently but the & logical operator should match the 2 conditions referring to this): 

  84684 #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  JP3048_for      JP3162_for      JP3171_for      JP3402_for      JP343_for       JP3539_for      JP3
  84685 scaffold440     420     .       T       G       999     PASS    DP=72;VDB=7.55993e-06;SGB=11.7312;RPB=0.0732065;MQB=0.00151772;MQSB=0.0740741;BQB=0.72433;MQ0F=0;AF1=0.1202
  84686 scaffold440     451     .       C       A       11.216  LowQual DP=71;VDB=0.0249187;SGB=-0.0412595;RPB=0.910489;MQB=0.70327;BQB=0.638446;MQ0F=0;AF1=0.0946915;AC1=10;DP4=35
  84687 scaffold440     452     .       C       A       10.3236 LowQual DP=71;VDB=0.02;SGB=-0.018177;RPB=1;MQB=0.162162;BQB=0.986486;MQ0F=0;AF1=0.0848011;AC1=9;DP4=37,0,2,0;MQ=42;
  84688 scaffold440     460     .       A       G       999     PASS    DP=71;VDB=3.01279e-43;SGB=10.0134;MQSB=0.0392157;MQ0F=0;AF1=1;AC1=112;DP4=0,0,51,2;MQ=43;FQ=-28.9555    GT:
  84689 Scaffold1210    18      .       C       T       17.1031 LowQual DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84690 Scaffold1210    23      .       A       G       17.1031 LowQual DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84691 Scaffold1210    30      .       A       G       17.1031 LowQual DP=5;VDB=0.0221621;SGB=0.913122;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AF1=0.62274;AC1=70;DP4=1,0,0,3;MQ=31;FQ=16.
  84692 scaffold420     41      .       T       G       14.1975 LowQual DP=2;SGB=-0.0045042;MQ0F=0;AF1=1;AC1=112;DP4=0,0,0,1;MQ=44;FQ=-22.7628  GT:PL:DP:SP:GQ  0/1:0,0,0:0:0:3 0/1
  84693 scaffold420     264     .       T       A       85.015  PASS    DP=4;VDB=0.0162466;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.6007   GT:PL:DP:SP
  84694 scaffold420     265     .       C       A       85.015  PASS    DP=4;VDB=0.0162466;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.6007   GT:PL:DP:SP
  84695 scaffold420     281     .       A       G       36.0512 PASS    DP=4;VDB=0.0138351;SGB=-0.0739942;MQSB=0.5;MQ0F=0;AF1=1;AC1=112;DP4=0,0,2,2;MQ=31;FQ=-24.5943   GT:PL:DP:SP
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written by beausoleilmo beausoleilmo

It may be worth trying an older version of vcftools, if that's a possibility. I just checked on version '0.1.12a' with --minDP 1, and it worked fine.

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written by berge2015 berge2015

I think you should be using one &. Per documentation:

FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample
FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
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written by igor igor

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