
Manuel Sérgio Sokolov Ravasqueira
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Latest activity by Manuel Sérgio Sokolov Ravasqueira-
Manuel Sérgio Sokolov Ravasqueira commented,
Thank you both. I converted both files with https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chain. And GATK Mutect2 ran with no problems.
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Manuel Sérgio Sokolov Ravasqueira commented,
Hi Anthony DiCi. I fixed this error by making in my case the -L and -V parameter the same. Can you clarify what changes when this happens?Thanks!
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Manuel Sérgio Sokolov Ravasqueira commented,
I found this: https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chainHowever this chainfile only has information of chromossome 1 to X and not the mitochondrial and other reg...
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Manuel Sérgio Sokolov Ravasqueira created a post,
GATK Mutect2 "--germline-resource" and "--panel-of-normals" for reference hg19
Dear GATK,I am using GATK Mutect2 (Gatk4) for variant calling having files with reference hg19. After reading extensively about this topic I understood that b37 is equivalente to hg19 thereby usin...
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Manuel Sérgio Sokolov Ravasqueira commented,
Dear GATK team, Thank you for this thread. I want to ask: I am applying the GATK Mutect2 over TargetSequecing over a set of genes and some genomic regions of interest without having PON of the the...
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Manuel Sérgio Sokolov Ravasqueira commented,
Hello, In the case of using hg19 human reference, where can I find a panel of normals similar to 1000g_pon.hg38.vcf to pass to this method? Best Regards, Manuel