rime
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Latest activity by rime-
rime commented,
Thanks very much. I've checked the bamout file by add --bam-output argument. Please look at the following IGV screenshots. Obviously, both variants do exist (MT:574 del and MT:574 A->C), most of th...
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rime created a post,
Some of variants detected by the Mutect2 are contradictory
Hi, I used GATK Mutect2 to detect the mitochondrial variant of the amplicon data, but I found that some adjacent Indel/SNP results were contradictory, as follows:version: Version：GATK4.1.8.1GATK co...
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rime created a post,
some Mito-mutations can't detected out right from amplicon data using Mutect2
Version: GATK4.1.6.0GATK commands: java -Xmx16g -Djava.io.tmpdir=./tmp -jar gatk-package-4.1.6.0-local.jar Mutect2 -R hs37d5.fa -L MT.bed --max-reads-per-alignment-start 0 --mitochondria-mode --kme...