how to filter and svtyper a normal tumor pair

[thelingxichen]

Hi,

Now I have normal vcf and tumor vcf produced by traditional lumpy seperately. To call genotype, should I: (1) svtyper normal vcf and tumor vcf seperately? (2) use bcftools merge the two vcf into a normal_tumor vcf first, and svtyper the merged vcf?

And for general filtering, is "DP > mean_coverage/5" suitable? Any other suggestion?

Thanks a lot.

[ryanlayer]

Merge first. I am not sure how bcftools merges SVs so you may want to look into that.

That DP seems okay too.

On Jul 23, 2018, at 9:28 PM, Paprika Chan notifications@github.com wrote:

Hi,

Now I have normal vcf and tumor vcf produced by traditional lumpy seperately. To call genotype, should I: (1) svtyper normal vcf and tumor vcf seperately? (2) use bcftools merge the two vcf into a normal_tumor vcf first, and svtyper the merged vcf?

And for general filtering, is "DP > mean_coverage/5" suitable? Any other suggestion?

Thanks a lot.

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[jianxinwang]

I used tumor normal pair for speedseq sv. Now I have both tumor and normal bam files and a two sample vcf file. How do I use SVTyper to make genotype calls? The usage for SVTyper only shows a single bam file.

[ryanlayer]

SVTyper can take multiple bams, but I like to speed this process up by doing the genotyping of the two samples in parallel, then using bcftools to merge the two resulting files into a final call set.

On Thu, Oct 11, 2018 at 9:00 AM jianxinwang notifications@github.com wrote:

I used tumor normal pair for speedseq sv. Now I have both tumor and normal bam files and a two sample vcf file. How do I use SVTyper to make genotype calls? The usage for SVTyper only shows a single bam file.

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[yaotianran]

@ryanlayer Do you mean that to be more accurate one should merge two vcf files first by bcftools and feed SVTyper two bam files to get the genotype, while to be faster one should do the genotyping seperately and then merge the results?

[ryanlayer]

Yep.

On Sun, Jul 12, 2020 at 7:37 PM Tianran YAO notifications@github.com wrote:

@ryanlayer https://github.com/ryanlayer Do you mean that to be more accurate one should merge two vcf files first by bcftools and feed SVTyper two bam files to get the genotype, while to be faster one should do the genotyping seperately and then merge the results?

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