Variant calling without matched normal sampleSingle-sample vs. joint genotypingAre soft-clipped bases used for variant calling in samtools + bcftools?BAM to BigWig without intermediary BedGraphCreating a new reference genome B by changing genome A with mismatches from BAM file without long readsIs it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?Merge 2 VCFs from different variant callersIssues performing variant calling with GATKHuman Genome Alignment and Variant Calling BenchmarksNo variant found using GATK 4.0 HaplotypeCallercalling diploid SNVs from long reads

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Variant calling without matched normal sample


Single-sample vs. joint genotypingAre soft-clipped bases used for variant calling in samtools + bcftools?BAM to BigWig without intermediary BedGraphCreating a new reference genome B by changing genome A with mismatches from BAM file without long readsIs it possible to use SNP heterozygosity as a proxy for Indel heterozygosity?Merge 2 VCFs from different variant callersIssues performing variant calling with GATKHuman Genome Alignment and Variant Calling BenchmarksNo variant found using GATK 4.0 HaplotypeCallercalling diploid SNVs from long reads













2












$begingroup$


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?










share|improve this question











$endgroup$
















    2












    $begingroup$


    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?










    share|improve this question











    $endgroup$














      2












      2








      2





      $begingroup$


      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?










      share|improve this question











      $endgroup$




      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?







      bam snp gatk wgs vcftools






      share|improve this question















      share|improve this question













      share|improve this question




      share|improve this question








      edited Mar 14 at 17:20







      Feresh Teh

















      asked Mar 14 at 14:25









      Feresh TehFeresh Teh

      44912




      44912




















          1 Answer
          1






          active

          oldest

          votes


















          6












          $begingroup$

          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.






          share|improve this answer











          $endgroup$












          • $begingroup$
            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?
            $endgroup$
            – Feresh Teh
            Mar 14 at 14:49






          • 3




            $begingroup$
            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.
            $endgroup$
            – Devon Ryan
            Mar 14 at 14:56










          • $begingroup$
            software.broadinstitute.org/gatk/documentation/article?id=11682
            $endgroup$
            – Feresh Teh
            Mar 18 at 17:54










          Your Answer





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          1 Answer
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          1 Answer
          1






          active

          oldest

          votes









          active

          oldest

          votes






          active

          oldest

          votes









          6












          $begingroup$

          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.






          share|improve this answer











          $endgroup$












          • $begingroup$
            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?
            $endgroup$
            – Feresh Teh
            Mar 14 at 14:49






          • 3




            $begingroup$
            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.
            $endgroup$
            – Devon Ryan
            Mar 14 at 14:56










          • $begingroup$
            software.broadinstitute.org/gatk/documentation/article?id=11682
            $endgroup$
            – Feresh Teh
            Mar 18 at 17:54















          6












          $begingroup$

          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.






          share|improve this answer











          $endgroup$












          • $begingroup$
            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?
            $endgroup$
            – Feresh Teh
            Mar 14 at 14:49






          • 3




            $begingroup$
            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.
            $endgroup$
            – Devon Ryan
            Mar 14 at 14:56










          • $begingroup$
            software.broadinstitute.org/gatk/documentation/article?id=11682
            $endgroup$
            – Feresh Teh
            Mar 18 at 17:54













          6












          6








          6





          $begingroup$

          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.






          share|improve this answer











          $endgroup$



          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.







          share|improve this answer














          share|improve this answer



          share|improve this answer








          edited Mar 14 at 14:56

























          answered Mar 14 at 14:42









          Devon RyanDevon Ryan

          14.2k21541




          14.2k21541











          • $begingroup$
            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?
            $endgroup$
            – Feresh Teh
            Mar 14 at 14:49






          • 3




            $begingroup$
            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.
            $endgroup$
            – Devon Ryan
            Mar 14 at 14:56










          • $begingroup$
            software.broadinstitute.org/gatk/documentation/article?id=11682
            $endgroup$
            – Feresh Teh
            Mar 18 at 17:54
















          • $begingroup$
            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?
            $endgroup$
            – Feresh Teh
            Mar 14 at 14:49






          • 3




            $begingroup$
            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.
            $endgroup$
            – Devon Ryan
            Mar 14 at 14:56










          • $begingroup$
            software.broadinstitute.org/gatk/documentation/article?id=11682
            $endgroup$
            – Feresh Teh
            Mar 18 at 17:54















          $begingroup$
          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?
          $endgroup$
          – Feresh Teh
          Mar 14 at 14:49




          $begingroup$
          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?
          $endgroup$
          – Feresh Teh
          Mar 14 at 14:49




          3




          3




          $begingroup$
          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.
          $endgroup$
          – Devon Ryan
          Mar 14 at 14:56




          $begingroup$
          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.
          $endgroup$
          – Devon Ryan
          Mar 14 at 14:56












          $begingroup$
          software.broadinstitute.org/gatk/documentation/article?id=11682
          $endgroup$
          – Feresh Teh
          Mar 18 at 17:54




          $begingroup$
          software.broadinstitute.org/gatk/documentation/article?id=11682
          $endgroup$
          – Feresh Teh
          Mar 18 at 17:54

















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