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?

Improve this question
$\endgroup$
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.

Improve this answer
$\endgroup$
3
  • $\begingroup$ 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 '19 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 '19 at 14:56
  • $\begingroup$ software.broadinstitute.org/gatk/documentation/article?id=11682 $\endgroup$
    – Exhausted
    Mar 18 '19 at 17:54
0
$\begingroup$

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

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.