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All tools in 'NGS: Indel Analysis' are missing on GVL-3.05:
NGS: Indel Analysis
- Filter Indels for SAM
- Indel Analysis Table for combining indel interval data
- Indel Analysis
One tool (Indel Anal…
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I run seGMM using command:seGMM -vcf /ddn/data/BDC/Analysis/NGS_Analysis/habusamra/230920_A00840_0041_AHGMT3DRX3/Alignment_Germline_Aziz/PBG-862-23_S3_HaplotypeCaller.vcf -i test.txt -a BAM -t WES -n…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…
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Hi,
Thanks very much for the great tool. We've been trying CRAQ out in several of our assembly projects and we sometimes run into strange behavior where analysis seems to finish ok, but low_confidenc…
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Should be a simple fix to ensure that the reference fasta file does not contain empty lines.
I'll likely fork the project soon anyways and will be happy to push the fix.
Trying to get a feel for the …
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Hello!
I wanted to express my gratitude for developing such excellent software! I recently assembled diploid haplotypes using pacbio hifi data, ont ultra long data, and hic data. I ran separate mer…
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Hello,
I am trying to incorporate the ensemble approach in my bcbio analysis and getting errors at the bcbio.variation command for validation of calls. Here are some details,
Run log -
/gpfs/ngs/on…
ssaif updated
9 years ago
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Dear Thierry et al.,
I am getting this error when I run assignR:
`Calibrating REF/ALT alleles...
Error in if (detect.gt == "GT_VCF_NUC") { : argument is of length zero`
when I try to run assi…
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As a bioinformatics analyst I want to generate a BED file from a gene panel for genomic test analysis so that I can use it as an input to an NGS pipeline tool.
- [ ] Get gene panel from panelapp, ref…
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hello
I have assembled two haplotypes using the hifiasm software based on HIC hifi ONT data. I am wondering if it is possible to utilize this software to inspect errors in the haplotype assemblies. I…