#mutect2 - Twitter Hashtag

almost 3 years ago

ℹ️It seems like "RNA-MuTect" is the gold standard tool for detecting #somatic #mutations from #RNAseq data. However, the documentation is really poor. ❓Are you aware of alternative tools for #somatic #mutation calling from #RNAseq data? #mutect #rnamutect #mutect2

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Nick Wong AU/MEL @methylnick

almost 5 years ago

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

methylnick's tweet photo. 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 https://t.co/dtq2gg9D4M

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Andrew Dhawan @andrewdhawan

over 5 years ago

Bash scripting and code optimization for clusters should be an olympic sport - the powerlifting of data science! 🏋️🏾Seriously tho, genomics tweeps: If anyone has a parallelized script for Mutect2 4.0.8.1 to run across chromosomes, plz let me know! #docsWhoCode #DNA #gatk #Mutect2

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Riyue Sunny Bao, PhD @RiyueSunnyBao

over 5 years ago

@IAnalyzeGenomes @Steen_Dr @nilshomer @MarkFleharty Yeah we have been using #MuTect2 for both WES and amplicon sequencing data. It has extremely good control on false positives, which is great for #Clinical #Sequencing. But #Vardict is more sensitive and rescue false negatives from #MuTect2 runs. We use both in our analysis.

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Riyue Sunny Bao, PhD @RiyueSunnyBao

over 5 years ago

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

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Riyue Sunny Bao, PhD @RiyueSunnyBao

almost 6 years ago

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

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Abhinav Jain @Abhinav_Jain_19

over 6 years ago

Systematic comparison of #SomaticVariant calling performance among different sequencing depth and mutation frequency. #Strelka2 and #Mutect2 #NGS @RcBHOYAR https://t.co/7R4vTCFGB9

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Seb Battaglia @Seb_Battaglia

over 8 years ago

@SMImmunology 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

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Prof Deborah Marsh @djmarsh24

almost 9 years ago

Our new #DataDescriptor paper out in #ScientificData on #TP53 #ovariancancer #HaplotypeCaller #MuTect2 #MPS https://t.co/ff5WdO6PAG

djmarsh24's tweet photo. Our new #DataDescriptor paper out in #ScientificData on #TP53 #ovariancancer #HaplotypeCaller #MuTect2 #MPS https://t.co/ff5WdO6PAG https://t.co/4sfeKjfQWZ

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