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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Problems on SURVIVOR merge #153

Open Ceonham opened 2 years ago

Ceonham commented 2 years ago

Hello,

I'm using SURVIVOR to merge SV results generated by Manta and Delly. Two input files both contain SV genotypes from 209 samples. But the output files only contains two sample genotype lines.

The command I used is: SURVIVOR merge list.txt 1000 2 1 1 0 50 merged_sv.vcf

My sample names in input files are: 19S669, 19S670, 19S671, ... , 19S878 Sample names in output files became: 19S669 19S669_1

I have no idea what these two genotype lines mean. And how does SURVIVOR deal with multi-sample genotypes from different softwares? Does it just merge SV sites but not genotypes? If so, do you have any suggestions what I should do to re-call genotypes according to these newly re-merged sites?

Thank you so much! Han Qin

sammyhansali commented 1 year ago

I have a similar problem. I used different softwares to generate my two input files. My input files have the same 259 samples yet the output only has two samples (second one is just the first sample name + "_1").

Were you able to find a fix?

Ceonham commented 1 year ago

It seems impossible to integrate two input files with so many samples by SURVIVOR. I suggest you to split your each of your input file into 259 individual files by bcftools. Then you could easily combine each two files for each sample. Finally you could use bcftools to combine all samples together. Hope this would be helpful. Han Qin

---------- Origin message ----------

From："Sammy Hansali" @.> To："fritzsedlazeck/SURVIVOR" @.> Subject：Re: [fritzsedlazeck/SURVIVOR] Problems on SURVIVOR merge (Issue #153) Date：2023-01-07 21:29:48I have a similar problem. I used different softwares to generate my two input files. My input files have the same 259 samples yet the output only has two samples (second one is just the first sample name + "_1").

Were you able to find a fix?

-- Reply to this email directly or view it on GitHub: https://github.com/fritzsedlazeck/SURVIVOR/issues/153#issuecomment-1374482356 You are receiving this because you authored the thread.

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sammyhansali commented 1 year ago

Thanks!