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https://github.com/gatk-workflows
https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels
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Hello All,
I'm trying to use Viva, however I'm stuck.
I'm running:
` julia viva -f /data1/i7-97_filtered_snps_final.vcf -t Default_Options -s png`
and getting this error:
Loading VCF file…
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I was investigating an issue where the depth is reported lower than expected at a given site. The default value of `--minimum-mapping-quality` is `20`, so I tried `1`, `20,` and `60`. Both values `1…
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ONT data does needs adapter chopping, quality filtering and length filtering. Adapter chopping for nanopore now references porechop, which is unmaintained as of 2018. Nanoflt is also recommended. I th…
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I am running sawfish-v0.12.2 on this bam file https://s3-us-west-2.amazonaws.com/human-pangenomics/working/HPRC_PLUS/HG002/analysis/aligned_reads/hifi/GRCh38/HG002_aligned_GRCh38_winnowmap.sorted.bam …
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=== Start HAHap phasing ===
Parameters: Minimum mapping quality = 0
Parameters: Threshold of low coverage = Median
Parameters: Minimum junction number = 4
Parameters: Likelihood of P1 and P2 = 0.4…
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Hello,
@dlaehnemann mentioned adding varlociraptor to a benchmark we have set up in #157, and I have some questions about recommendations for setting that up.
We currently have an internal bench…
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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…
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Hello,
is it possible to optimize the memory efficency? I have a 60GB RAM server but the training failes because the RAM is full after the message "Deriving top level model" "cannot allocate vector o…
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Hi there,
Thanks for developing this tool!
I was trying to run minimap2-aligned BAM files with Sawfish and encountered an error saying 'no rq tag'. I checked PacBio's doc and found it is the tag…