User: sbilobram

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sbilobram10
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New User
Location:
Canada
Last seen:
4 months, 2 weeks ago
Joined:
4 years, 11 months ago
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s********@bcgsc.ca

Posts by sbilobram

<prev • 5 results • page 1 of 1 • next >
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Strelka2 and single tumour sample
... Is there a variant calling tool for a single tumour sample in Strelka? That is there is NO matched Normal for the FFPE exome sample that I wish to find variants on. Any Suggestions? ...
variant calling written 6 months ago by sbilobram10
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Comment: A: strelka2 vs strelka1
... In both cases configureStrelkaSomaticWorkflow.py is run with matched normal and tumour bams and the hg19a.fa reference. No other switches were applied. The STRELKA2 run also is provided with the *--indelCandidates ./MANTA_ANALYSIS_PATH/results/variants/candidateSmallIndels.vcf.gz* which STRELKA1 ...
written 14 months ago by sbilobram10
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strelka2 vs strelka1
... we are possibly planning a switch to Strelka2 from Strelka1 but tests are showing performance is poorer. Specifically for the same data set STRELKA2.9.2 specificity and sensitivity measures are significantly lower than what we were seeing with STRELKA1.0.14. In both cases default options were used ...
snp callers written 14 months ago by sbilobram10 • updated 14 months ago by Chris Saunders180
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small indel caller requested
... Besides GATK, Pindel and Dindel are there any other recommended tools to call somatic indels less than 1000bp?   I know this question has been asked many times and I have seen the posts to the thread: Question: Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data Bu ...
indel caller sequencing written 3.8 years ago by sbilobram10
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V4 illumina Sequencer
... We are currently using V4 Illumina Sequencers.  I am trying to estimate optical duplicates and to do so I have recently upgraded PicardTools to V 1.122 to enable readname abilty.  The generated metrics file now outputs a non-zero value for READ_PAIR_OPTICAL_DUPLICATES which seems reasonable. When I ...
alignment rna-seq optical_duplicates sequencing written 4.9 years ago by sbilobram10

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Popular Question 14 months ago, created a question with more than 1,000 views. For V4 illumina Sequencer

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