
manolis
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Activity overview
Latest activity by manolis-
manolis created a post,
Conda for GATK4
REQUIRED for all errors and issues: a) GATK version used: 4.6.1.0b) Exact command used: python -c "import vqsr_cnn" Hi, not sure if it is an installation issue from my side, but after conda install...
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manolis created a post,
Dragen-mode HaplotypeCaller - zygosities
a) GATK v4.3.0.0 b) Exact command used: Bash pipeline locally created be me to run WES # Dragen Haplotypecaller Functional Equivalent ${GATK} HaplotypeCaller \-R ${ref} \-I ${after-DRAGEN-STR-Model...
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manolis commented,
Hi Genevieve, thank you very much! Best regards
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manolis created a post,
WDL pipeline: Mitochondrial-short-variant-discovery
AnsweredHi, where can I find (link) the Mitochondrial-short-variant-discovery WDL pipeline? It is not under best-practice, and I just found an old one. Best
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manolis commented,
Hi, the last time I used this pipeline is months ago ... does BQSR work with the GRCh38.primary_assembly.genome.fa? About design, you can just take all exons coordinates from a Gencode/RefSeq datab...
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manolis commented,
Hi Ayam Gupta , with STAR and BQSR I used GRCh38.primary_assembly.genome.fa Sorry for my late answer!
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manolis commented,
Hi Ayam Gupta, what is your issue with the pipeline?
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manolis commented,
Hi Pamela Bretscher, thank you. Best
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manolis created a post,
HaplotypeCaller and Mutect2 used for SARS-Cov-2
Hi, I would like to ask you if I can use HC or Mutect2 for SARS-Cov-2 variant calling. Do you have any experience? Best
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manolis commented,
H iGenevieve Brandt (she/her), no, was just a curiosity considering that in RNAseq the target coverage and uniformity depend on the gene expression levels and in many cases some and different genes...