BQSR and VQSR resource for CHM13 (T2T) genome assembly
Hello! I am now mapping NGS data to the CHM13 (T2T) genome. I wonder how to perform BQSR and VQSR for I cannot find the resource of known sites for the CHM13 (T2T) genome. Does anyone know how to do that? Thank you in advance!
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Thank you for your post, Jacob Wang ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi, Anthony! Thank you for your quick response. I understand the support policy and I will wait for the updates.
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Hi Jacob Wang,
Thank you for writing to the GATK forum! I hope that we can help you sort this out.
If you can find a VCF for your sample within a line, you can use it. We have a tool, LiftoverVcf (Picard), that will allow you to “lift over” a VCF from one genome build to another; this assumes you have the proper chain file.
I hope this helps! Please let me know if this leads you to success. If any other questions arise, please do not hesitate to reach out.
Best,
Anthony -
Hi Jacob Wang,
We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!
Kind regards,
Anthony
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Hello, I have a follow up question on it:
Suppose, I have already aligned my FASTQ files and used MD, BQSR, ApplyBQSR and Haplotypecaller to generate VCF with GRCh38 through GCP sites resources.
If I want to benchmark my dataset with CHM13 instead of GRCh38 to see the differences, Do I need to just use LiftoverVcf (Picard), with my old GRCh38 generated VCF to get another new VCF for CHM13 variants? Right? Can you please explain what other steps should I follow to benchmark GATK with both GRCh38 and CHM13? Thanks.
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Hi Tanveer Ahmad,
You can either lift your vcf over using LiftoverVcf, or reprocess your data using the T2T reference instead of hg38.
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