<p>If you just want to filter out calls present in dbSNP then use:</p>

<pre><code>java -jar GenomeAnalysisTK.jar \
   -T SelectVariants \
   -R reference.fasta \
   -V patient.vcf \
   --discordance dbSNP.vcf \
   -o patient.filtered.vcf
</code></pre>

<p><code>--discordance</code> will produce calls not present in dbSNP.</p>

CC BY-SA 4.0
2019-03-14T14:49:44.157Z
Thanks a lot @Devon, Calling SNV and indel in many tools returns vcf but I called copy number by varscan that did not return .vcf output, is this command is applicable yet?
Zizogolu
CC BY-SA 4.0
2019-03-14T14:56:55.237Z
It's usually best to mention things like that in your post... I presume this will still work, but I can't say I've ever tried.
Devon Ryan
CC BY-SA 4.0
2019-03-18T17:54:11.643Z
https://software.broadinstitute.org/gatk/documentation/article?id=11682
Zizogolu
CC BY-SA 4.0
2022-01-26T15:11:47.523Z
I heard GenomeAnalysisTK.jar has been replaced. Do you know by which function we can filter a vcf file based on dbSNP?
Zizogolu
CC BY-SA 4.0
2019-03-14T14:42:15.717Z
2019-03-14T14:56:20.050Z
2019-03-14T14:56:20.050Z
Devon Ryan
<p>Here is a clue by scatngs</p>

<p><a href="https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs" rel="nofollow noreferrer">https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs</a></p>

<p>and already calculated file is here </p>

<p><a href="ftp://ftp.sanger.ac.uk/pub/cancer/support-files/CPIB/ascatNgs/Human/GRCh37/" rel="nofollow noreferrer">ftp://ftp.sanger.ac.uk/pub/cancer/support-files/CPIB/ascatNgs/Human/GRCh37/</a></p>

<p>Although installing scatngs itself is a big burden </p>

CC BY-SA 4.0
2019-03-27T14:53:39.453Z
2019-03-27T14:53:39.453Z
Zizogolu
<p>I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), how I can use read counts at germline heterozygous positions estimated by GATK 3.2-2 to compensate for the absence of matched normal sample? I heard people use dbsnp VCF instead of the matched normal small variant VCF. But, I don't know start from where? which GATK function does that?</p>

<blockquote>
  <p>I should mention, Calling SNV and indel in many tools returns vcf but
  I called copy number by varscan that did not return .vcf output so I
  am not sure what to do for CNV</p>
</blockquote>

<p>Any helps please?</p>

<sam><snp><gatk><wgs><vcftools>
Variant calling without matched normal sample
# Variant calling without matched normal sample

(Asked by: username_0 on 2019-03-14)

I have WGS .bam files for 3 patients (tumour and its matched derived model namely organoid) but I don't matched normal sample. If I call variants of each patients (tumour and its matched organoid), how I can use read counts at germline heterozygous positions estimated by GATK 3.2-2 to compensate for the absence of matched normal sample? I heard people use dbsnp VCF instead of the matched normal small variant VCF. But, I don't know start from where? which GATK function does that?

> I should mention, Calling SNV and indel in many tools returns vcf but
> I called copy number by varscan that did not return .vcf output so I
> am not sure what to do for CNV

Any helps please?

**Tags:** sam, snp, gatk, wgs, vcftools

---

## 2 answers

### Answer by username_1 on 2019-03-14. Score: 6

If you just want to filter out calls present in dbSNP then use:
java -jar GenomeAnalysisTK.jar \
   -T SelectVariants \
   -R reference.fasta \
   -V patient.vcf \
   --discordance dbSNP.vcf \
   -o patient.filtered.vcf

--discordance will produce calls not present in dbSNP.

> **Comments:**
> **username_0**: Thanks a lot @Devon, Calling SNV and indel in many tools returns vcf but I called copy number by varscan that did not return .vcf output, is this command is applicable yet?  
> **username_1**: It's usually best to mention things like that in your post... I presume this will still work, but I can't say I've ever tried.  
> **username_0**: https://software.broadinstitute.org/gatk/documentation/article?id=11682  
> **username_0**: I heard GenomeAnalysisTK.jar has been replaced. Do you know by which function we can filter a vcf file based on dbSNP?  

---

### Answer by username_0 on 2019-03-27. Score: 0

Here is a clue by scatngs

<https://github.com/cancerit/ascatNgs/wiki/Human-reference-files-from-1000-genomes-VCFs>

and already calculated file is here

<ftp://ftp.sanger.ac.uk/pub/cancer/support-files/CPIB/ascatNgs/Human/GRCh37/>

Although installing scatngs itself is a big burden


---

