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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?

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2 Answers 2

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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.

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  • $\begingroup$ 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? $\endgroup$
    – Exhausted
    Mar 14, 2019 at 14:49
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    $\begingroup$ 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, 2019 at 14:56
  • $\begingroup$ software.broadinstitute.org/gatk/documentation/article?id=11682 $\endgroup$
    – Exhausted
    Mar 18, 2019 at 17:54
  • $\begingroup$ I heard GenomeAnalysisTK.jar has been replaced. Do you know by which function we can filter a vcf file based on dbSNP? $\endgroup$
    – Exhausted
    Jan 26 at 15:11
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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

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