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Hi, I'm new to snakemake, and have no idea of submitting Scanneo2 jobs to HPC. Any instructions would be very helpful! Thanks!
Regards,
Xiao
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Hi Dave,
I try to genotype bunch of samples with svtools lsort, svtools lmerge and svtools genotype.
I try to genotype around 1.2k samples with svtools. If I downsample this collection for examp…
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Greetings,
I have gvcf files already generated from deepvariant and I have a vcf file of bi-allelic snps Im interested in genotyping. Ive been trying to find if a method exists to genotype snp si…
bwubb updated
9 months ago
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Hi!
Thank you for this extremely useful tool.
I have just used `gtc2vcf` to convert 300 GTC files from `Infinium Global Screening Array` into VCF.
```
bcftools +gtc2vcf
-Ov \
--adjust-cl…
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Dear @eblerjana,
Thank you for this useful tool. I have a question about Pangenie installation.
#h**ere is the pangenie installation method I chose**
git clone https://github.com/eblerjana/pa…
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On this page:
https://github.com/dnanexus/UKB_RAP/tree/main/end_to_end_gwas_phewas/liftover_plink_beds_tmp
It says:
"In order to perform association testing with the sequncing data on step-2, it is…
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I'm struggling getting some illumina genotypes to load. I've converted the gtreports to lgen format but keep getting the 3+ allele error. In the example below all that's there is A and 0. Specifying `…
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Hi,
I am interested in genotyping around SNP sites +/- 1 kb. Which bin size should I use? Is 100 bp ok?
Thanks.
gevro updated
9 months ago
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(Part of review thread https://github.com/openjournals/joss-reviews/issues/6062)
Overall, the paper reads well, and I am convinced of your pipeline's value both in terms of
need for the community…
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Hi there,
I have tried genotyping with CRAM file using Aldy.
But I have a issue.
$ aldy genotype -p wgs -g ifnl3 1_HB00001.cram --reference GRCh38.p12.genome.fa -o test_1_HB00001-ifnl3.aldy
🐿…