#mutect2 search results
and to top off my morning, nothing better than to see a test script run for 1,013.78 minutes with the output returning SUCCESS! @gatk_dev #Mutect2 #notonlyabioinformatician
#Mutect2 がいつの間にか変わっていて使いやすくなったのは良いのだけど、dbSNPの情報が入れられなくなっている。broadの人たちは--germline-resourceとしてgnomADを使えって言ってるけど、犬には無いんだ(´・ω・`)
Combination of #MuTect2, #Strelka #Bambino and #VarScan due to the variability of each single one. We measure via #WES, whole genome is too expensive for routine studies
Using #GATK4 #MuTect2 on #targeted #amplicon #sequencing data: - lift target BED to #GRCh38 w #picard (ref allele consistency) - bump --max-reads-per-alignment-start to 500 - no markdup if not UMI - pay close att to each amplicon cov - use tumor/normal pairs #BioInformatics
For tumor-only #variant calling, I'd like to take into account the clonality while calling variants - #pureCN is great, but cannot get it to work with #Mutect2 #VCFs w latest #GATK4. Any alternatives?? :) #bioinformatics #cancer #somatic #mutation
Wonder if there any @broadinstitute @broadgenomics GATK Workshop in EU?Interested to enrich knowledge on #RNAseq #SomaticVariant #MuTect2
Any #MuTect2 experts out there who can explain this strange behavior? @gatk_dev gatkforums.broadinstitute.org/gatk/discussio…
Systematic comparison of #SomaticVariant calling performance among different sequencing depth and mutation frequency. #Strelka2 and #Mutect2 #NGS @RcBHOYAR nature.com/articles/s4159…
#Mutect2 がいつの間にか変わっていて使いやすくなったのは良いのだけど、dbSNPの情報が入れられなくなっている。broadの人たちは--germline-resourceとしてgnomADを使えって言ってるけど、犬には無いんだ(´・ω・`)
and to top off my morning, nothing better than to see a test script run for 1,013.78 minutes with the output returning SUCCESS! @gatk_dev #Mutect2 #notonlyabioinformatician
Using #GATK4 #MuTect2 on #targeted #amplicon #sequencing data: - lift target BED to #GRCh38 w #picard (ref allele consistency) - bump --max-reads-per-alignment-start to 500 - no markdup if not UMI - pay close att to each amplicon cov - use tumor/normal pairs #BioInformatics
For tumor-only #variant calling, I'd like to take into account the clonality while calling variants - #pureCN is great, but cannot get it to work with #Mutect2 #VCFs w latest #GATK4. Any alternatives?? :) #bioinformatics #cancer #somatic #mutation
Systematic comparison of #SomaticVariant calling performance among different sequencing depth and mutation frequency. #Strelka2 and #Mutect2 #NGS @RcBHOYAR nature.com/articles/s4159…
Combination of #MuTect2, #Strelka #Bambino and #VarScan due to the variability of each single one. We measure via #WES, whole genome is too expensive for routine studies
Wonder if there any @broadinstitute @broadgenomics GATK Workshop in EU?Interested to enrich knowledge on #RNAseq #SomaticVariant #MuTect2
Any #MuTect2 experts out there who can explain this strange behavior? @gatk_dev gatkforums.broadinstitute.org/gatk/discussio…
and to top off my morning, nothing better than to see a test script run for 1,013.78 minutes with the output returning SUCCESS! @gatk_dev #Mutect2 #notonlyabioinformatician
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