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GATK gtf file

AswathyNAswathyN BangaloreMember

Hello,
I am using human_g1k_v37.fasta from GATK as a reference file for my Targeted Sequence Analysis.
I am using Homo_sapiens.GRCh37.75.gtf for making my interval file.
I understand there are a few differences between NCBI fasta sequence and the fasta by GATK.
Is there a gtf file from GATK that can is compatible with the fasta file provided by GATK.

Thanks,
Aswathy

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by Sheila

Issue Number
176
State
closed
Last Updated
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vdauwera

Best Answer

Answers

  • AswathyNAswathyN BangaloreMember

    Thank you Geraldine.. I am using NCBI gtf file for creating bed file. I was lil concerned about the unplaced contigs. But I think now it is in a "Good to go" stage.. Thanks again..

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