Request for Chain File from Full hg19 Reference Genome to hg19 Masked Reference Genome
Isra Nurhassen
Dear Genome Browser Team,
I am currently working on a project that involves the liftover of GVCF files, which were originally mapped to the full hg19 reference genome, to the hg19 masked reference genome. To facilitate this process, I am in need of the chain file that allows for the conversion between these two reference genomes.
Could you please provide the chain file required for this operation? Additionally, any guidance or resources you can share regarding the best practices for performing this liftover would be greatly appreciated.
Thank you very much for your assistance.
Best regards,
Isra Nurhassen
PhD candidate
TWINCORE institute
Gerardo Perez
Hello, Isra.
Thank you for your interest in the UCSC Genome Browser.
Could you provide more details on what you are trying to do? Which hg19 masked reference genome are you referring to?
Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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Isra Nurhassen
Dear Genome Browser Team,
Thank you very much for your fast reply.
My goal is to combine GVCF files with combineGVCF of GATK. Some were mapped against unmasked hg19, others to a masked hg19 reference genome.
I am trying to convert some GVCF files which were mapped to a unmasked hg19 version to a masked hg19 reference genome (hg19_noalt_masked.fa).
Isra
--------------------Ursprüngliche Nachricht--------------------
Von: Gerardo Perez <gpe...@ucsc.edu>
Gesendet: Freitag 19. Juli 2024 8:10
An: Isra Nurhassen <isra.nu...@twincore.de>
CC: gen...@soe.ucsc.edu
Betreff: Re: [genome] Request for Chain File from Full hg19 Reference Genome to hg19 Masked Reference Genome
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