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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?

bam snp gatk wgs vcftools

share|improve this question

edited Mar 14 at 17:20

Feresh Teh

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

$endgroup$

add a comment | 

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?

bam snp gatk wgs vcftools

share|improve this question

edited Mar 14 at 17:20

Feresh Teh

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

$endgroup$

add a comment | 

$begingroup$

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?

bam snp gatk wgs vcftools

share|improve this question

edited Mar 14 at 17:20

Feresh Teh

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

$endgroup$

share|improve this question

edited Mar 14 at 17:20

Feresh Teh

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

share|improve this question

edited Mar 14 at 17:20

Feresh Teh

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

asked Mar 14 at 14:25

Feresh TehFeresh Teh

44912

asked Mar 14 at 14:25

Feresh TehFeresh Teh

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

edited Mar 14 at 14:56

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  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
  

  
  
  
  

add a comment | 

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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

edited Mar 14 at 14:56

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  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
  

  
  
  
  

add a comment | 

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

edited Mar 14 at 14:56

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

$endgroup$

• 
  
  
  

  
  

  
  
  
  
  
  

  
  $begingroup$
  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
  

  
  
  
  

add a comment | 

$begingroup$

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

edited Mar 14 at 14:56

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

$endgroup$

java -jar GenomeAnalysisTK.jar 
 -T SelectVariants 
 -R reference.fasta 
 -V patient.vcf 
 --discordance dbSNP.vcf 
 -o patient.filtered.vcf

share|improve this answer

edited Mar 14 at 14:56

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541

answered Mar 14 at 14:42

Devon Ryan♦Devon Ryan

14.2k21541