Multi-sample VCF for CNV calling
Answered
Hi, I'm using GATK 4.1.9.0 for Germline and Rare copy number variant discovery.
I have a big dataset of more than 400 samples and I'm studying about 800 genes in each sample. I ran CNV pipeline successfully but unfortunately problem is to handle data at PostprocessGermlineCNVCalling stage. Because this tool give results for only 1 sample at a moment. Is there any way to make multi-sample VCF rather than making separate VCF file for each sample? Just like GenomicsDBImport!
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Official comment
Thank you for your post. We keep track of these feature requests so our developers can use them when improving the GATK tools. I encourage other users who could use this feature to interact with this post so that it gets more attention!
In regards to running our gCNV pipeline on many samples, I would recommend checking out our WDLs. They are meant to be optimized for many samples. Specifically for what you are looking to do, I would recommend checking out the joint_call_exome_cnvs.wdl.
Hope this helps!
Genevieve
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Genevieve Brandt (she/her) thank you for your suggestion.
I already finished this task by writing a bash script. I hope using WDLs will be helpful for other people trying to do similar analysis.
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Thanks for the update Muhammad Shoaib Akhtar!
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Dear Muhammad Shoaib Akhtar
I would be interested to try your bash script. I am facing the same problem.
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Faisal Almalki it's s;imple. Please use bgzip, tabix and bcftools merge.
I added my script below:
#!/bin/sh
ls
for i in `ls -d gen*.vcf`;do
echo $i
bgzip $i
done
for j in `ls -d gen*.vcf.gz`;do
echo $k
tabix $j
done
bcftools merge -l list_of_vcf.gz -o output.vcf.gzgen*.vcf is output of genotyped intervals in PostprocessGermlineCNVCalls. You may run similarly for segments.
Goodluck
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Thank you for providing your solution Muhammad Shoaib Akhtar!
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thank you for the script. Its really helpful
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