Changes

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDQ 7

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDQ 7

* Example 1: using --minDepth 10 to output de novo calls for which all three individuals (father, mother and child) have depth >=10.

* Example 3: using --minDepth 10 to output de novo calls for which all three individuals (father, mother and child) have depth >=10.

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDepth 10

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDepth 10

* Example 1: using --minTotalDepth 1000 to filter sites that have a total reads less than 1000. This option will filter the entire site.  

* Example 4: using --minTotalDepth 1000 to filter sites that have a total reads less than 1000. This option will filter the entire site.  

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minTotalDepth 1000

  triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minTotalDepth 1000