Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-14T14:49:44.157Z
Answers.Text: 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?
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-14T14:56:55.237Z
Answers.Text: 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.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-18T17:54:11.643Z
Answers.Text: https://software.broadinstitute.org/gatk/documentation/article?id=11682
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-01-26T15:11:47.523Z
Answers.Text: I heard GenomeAnalysisTK.jar has been replaced. Do you know by which function we can filter a vcf file based on dbSNP?
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-14T14:42:15.717Z
Answers.LastActivityDate: 2019-03-14T14:56:20.050Z
Answers.LastEditDate: 2019-03-14T14:56:20.050Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-27T14:53:39.453Z
Answers.LastActivityDate: 2019-03-27T14:53:39.453Z
Answers.UserDisplayName: Zizogolu
Body: <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>
  
Tags: <sam><snp><gatk><wgs><vcftools>
Title: Variant calling without matched normal sample
ThreadText: # 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 @username_1, 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
  
  
  ---
  
  