Amy zhang
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Latest activity by Amy zhang-
Amy zhang commented,
Hi Genevieve, The program log what you need from HaplotypeCaller from the original (not called) and downsampled bams(called) as fallowing: 1.The program log from HaplotypeCaller from the original b...
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Amy zhang commented,
Hi Genevieve, I'm trying modify the parameters --kmer-size([20-35]) and --max-num-haplotypes-in-population(1024). It works on this site. But I don't know if it cause other sites different. I know t...
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Amy zhang commented,
Hi Genevieve, The second point which you mentioned was used. The other two points will provide later. thanks a lot, Amy
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Amy zhang commented,
Hi Genevieve, Thanks for your reply. Before writing this post, I have red the troubleshooting article for this type of question: When HaplotypeCaller and Mutect2 do not call an expected variant. I...
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Amy zhang created a post,
Abnormal Results from GATK HaplotypeCaller --different variant Call from the fastq and its downsample fastq from the same fastqdata
AnsweredDear Genevieve， I have a PE fastq from a multiprimer Panel. When I use the same commandline(see the code) and parameters analysising the raw fastq and downsample fastq. I get different results seei...