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
$begingroup$
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
asked 7 hours ago
Feresh TehFeresh Teh
44112
$endgroup$
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
asked 7 hours ago
Feresh TehFeresh Teh
44112
$endgroup$
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
asked 7 hours ago
Feresh TehFeresh Teh
44112
$endgroup$
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
bam snp gatk wgs vcftools
asked 7 hours ago
Feresh TehFeresh Teh
44112
asked 7 hours ago
Feresh TehFeresh Teh
44112
edited 4 hours ago
Feresh Teh
asked 7 hours ago
Feresh TehFeresh Teh
44112
asked 7 hours ago
Feresh TehFeresh Teh
44112
asked 7 hours ago
Feresh TehFeresh Teh
44112
44112
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
$begingroup$
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.
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
$endgroup$
$begingroup$
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
7 hours ago
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♦
7 hours ago
add a comment |
Your Answer
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1 Answer
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oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
$begingroup$
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.
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
$endgroup$
$begingroup$
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
7 hours ago
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♦
7 hours ago
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.
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
$endgroup$
$begingroup$
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
7 hours ago
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♦
7 hours ago
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.
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
$endgroup$
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.
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
edited 7 hours ago
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
answered 7 hours ago
Devon Ryan♦Devon Ryan
14k21540
14k21540
$begingroup$
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
7 hours ago
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♦
7 hours ago
add a comment |
$begingroup$
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
7 hours ago
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♦
7 hours ago
$begingroup$
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
7 hours ago
$begingroup$
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
7 hours ago
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♦
7 hours ago
$begingroup$
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♦
7 hours ago
add a comment |
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