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What is the good or stringent parameter for variant calling?
At present using the DP > 10 and Q > 30 for Variant calling. Is it ok?

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  • $\begingroup$ What tool are you using and what are you calling on, whole genome, exome? $\endgroup$ – CKM Jun 28 '16 at 14:19
  • $\begingroup$ @CMosychuk, its Whole genome sequencing $\endgroup$ – Krithi.S Jun 29 '16 at 5:05
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We will be needing some additional information to answer your question more completely:

What sequencing platform are you using? Illumina HiSeq/MySeq; Ion proton

What type of sequencing (as noted by @CMosychuk): Exome or Whole Genome?

What type of variant caller (as noted by @CMosychuk): Unified Genotyper; Haplotype Caller; TVC

The QUAL metric is heavily dictated my sequencing depth, so if you use 30 (phred-scaled), that would be an accuracy of 99.9%.

The typical QUAL metric used by most sequencing studies is 20 so using 30 may cause accumulation of false negatives. But again, depends on the type of sequencing and platform used.

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  • $\begingroup$ this looks more like a comment than an answer - once you have earned some more reputation points you will be able to comment anywhere, but until then please refrain from commenting as an "answer" - thanks for your contribution! $\endgroup$ – Vance L Albaugh Jun 28 '16 at 23:00
  • $\begingroup$ @VanceLAlbaugh I won't classify this as a comment outright, the latter parts of the answer are in fact answers to the question. $\endgroup$ – March Ho Jun 29 '16 at 0:27
  • $\begingroup$ @MarchHo I'll take your word for it - not obvious to me (an outsider in that specific field) $\endgroup$ – Vance L Albaugh Jun 29 '16 at 0:36
  • $\begingroup$ Its whole genome sequencing, Illumina HiSeq 1000 platform, Type of cariant caller is Unified genotyper. Tools using samtool, vcftool. $\endgroup$ – Krithi.S Jun 29 '16 at 5:04
  • $\begingroup$ For variant filter using SNPeff $\endgroup$ – Krithi.S Jun 29 '16 at 5:05

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