Having trouble getting non-empty output

I'm trying to run denovogear on a WGS trio, and I'm not getting any variants in the output file. I'd appreciate any suggestions of what I may be doing wrong.

Our samples are called WG0840 (proband), WG0841 (mother), and WG0842 (father), and they were sequenced with 100bp paired-end reads with mean read depth of 50X on a BGISeq-500. The reads were aligned with BWA MEM (version 0.7.15), and processed with Picard (version 2.7.1, FixMateInformation, MarkDuplicates), and GATK (version 3.7, RealignerTargetCreator, IndelRealigner). I have denovogear version 1.1.1, and samtools 1.9. I'm running the command:

samtools mpileup -r 1:170120000-170140000 -f human_g1k_v37.fasta -gD WG084[012].bam | denovogear-v1.1.1-Linux-x86_64/bin/dng dnm auto --bcf - --pp_cutoff 0.0001 --ped WG0840-WG0841-WG0842_2.ped --output_vcf WG0840-WG0841-WG0842_denovogear_samtools.vcf

and WG0840-WG0841-WG0842_2.ped contains just one line:

WG0840 WG0840 WG0842 WG0841 1 1

I receive the following output on the console:

DeNovoGear v1.1.1

posterior probability cutoff: 0.0001
output vcf file: WG0840-WG0841-WG0842_denovogear_samtools.vcf
Created SNP lookup table
 First mrate: 1 last: 1
 First code: 6 last: 6
 First target string: AA/AA/AA last: TT/TT/TT
 First tref: 0.0002388 last: 0.99301

Created indel lookup table First code: 6 last: 6
 First target string: RR/RR/RR last: DD/DD/DD
 First prior: 0.05 last: 0.114

Created paired lookup table
 First target string: AA/AA last: TT/TT
 First prior 1 last: 1
[warning] samtools mpileup option `g` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[warning] samtools mpileup option `D` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[mpileup] 3 samples in 3 input files

Total number of SNP sites interrogated: 0
Total number of SNP sites passing read-depth filters: 0
Total number of INDEL sites interrogated: 0
Total number of INDEL sites passing read-depth filters: 0
Total number of Paired sample sites interrogated: 0
Total number of Paired sample sites passing read-depth filters: 0
Done !

But the vcf file does not contain any variants.

I know I have a de novo variant at 1:170,129,733, and it shows up very nicely in the samtools mpileup, but doesn't appear in the output file from denovogear. If I run:

samtools mpileup -r 1:170129733-170129735 -f human_g1k_v37.fasta r03_assembly/WG084[012].bam

then I get the following output:

1   170129733   C   43  ...,..,,,.,,,,,,.,..,,,,,..,.,,,,..,,,...,^].   BFiGFGFFEFFF@FFEFFGDFDGEGFGFFFFFFFGF?G=FFFE 47  ...,.,,,,......,.,.,,,....,,......,..,,.,,..,,. lFFFFFFFEFFFGFGGlGEFFFFFGFGFF=GFFGFFFGFCBFDCFFE 55  ,$,......,.,.,......,.......,....,...,,,...,,.,,,..,,.,^].  >FFFGGFFFFFFF;GGEmDAGFGFlFGBFF?G?EGGFGFGGFGFEEBF@G;FGEE
1   170129734   A   42  .GgGGgg,.,,gg,g.,G.gg,,,.G,G,,ggGG,g,G..g.  FkGFFFFEFFFBGFFFF?FGDGFEFGFEFFGBFFEFFDFGFF  47  .$.$.,.,,,,......,.,.,,,....,,......,..,,.,,..,,.   c;FFFFFFE1F>:FFFlFECFFGFGFGEFDFFGAFFFGF>AFEE@FE 56  ,......,.,.,.T....,.......,....,.,..,,,...,,.,,,..,,.,.^].  FFEDFFFFE7FFFECGlE9EFDFkFEFGGGFFE@GFFFFFFFGGGFF@FFGFFEGB
1   170129735   A   44  ..,..,,,.,,,,,,.,..,,,,,..,.,,,,..,,,...,..^].  FkEFFFFFFFF?GFFFFFFFFGFFFFFD=FCGFFFFFCFFGF7E    46  .,.,,,,......,.,.,,,....,,.....,.,..,,.,,..,,.  FFCFFFFFBF?EFGkGFGFFFGFFEEFFFFFEGGFFGFC@FF8FFF  56  ,......,.,.,.T....,.......,....,.,..,,,...,,.,,,..,,.,..    GFDGFDF:FAFFEDFFk?EFFGFhAFGFFFGGF4FFFEFFFFFGFFFFFFGFFFFE

Any suggestions would be appreciated.

ultimatesource / denovogear

Having trouble getting non-empty output #307