Pierre_Bioinfo
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Activity overview
Latest activity by Pierre_Bioinfo-
Pierre_Bioinfo created a post,
Miscalled variant with haplotypecaller and question about –linked-graph-de-bruijn
REQUIRED for all errors and issues: a) GATK version used: 4.2.0.0b) Exact command used: /opt/tools/gatk-4.2.0.0/gatk --java-options -Xmx10G HaplotypeCaller -I /data/results/EXOME_185_EEQ3542/bam/24...
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Pierre_Bioinfo commented,
Dear Ricky, Thank you for your clear answer! It confirms the way I understood the meaning of these metrics.However I have made an observation I cannot explain which makes me feel that I did not ful...
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Pierre_Bioinfo created a post,
Explanation on the HS Penalty metric
REQUIRED for all errors and issues: a) GATK version used: 4.2.0.0 b) Exact command used: /usr/bin/java -Xmx2G -jar /opt/tools/picard.jar CollectHsMetrics -I 235109_S6.bam -O metrics_235109_S6.tx...
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Pierre_Bioinfo commented,
Hello, That's my command: /path/to/GATK(4.2.0.0) VariantEval --eval /my/VCF/file -D dbsnp_146.hg38.vcf.gz -L bedFile.interval_list -no-ev true -EV CompOverlap -EV TiTvVariantEvaluator -O ${sampl...
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Pierre_Bioinfo commented,
Thanks for your answer Genevieve ! I just test your solution and I have same value with SelectVariant and my total number of variants in my VCFs ... I don't really understand why I have this result...
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Pierre_Bioinfo created a post,
GATK VariantEval no concordance between dbSNP and our data
AnsweredHi, I use VariantEval to calculate the percentage of variant present in dbSNP. So when I use VariantEval, with CompOverlap I have this result in nEvalVariants: Novelty nEvalVariants all ...