Whole Genome Sequencing
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How to use R-based PLINK plug-in in RAP?
- Former User of DNAx Community_26
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Best approach annotating variants with CADD and gnomAD
- Former User of DNAx Community_29
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SNP IDs in WGS
- Former User of DNAx Community_56
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I am trying to find WGS vcf files. I see individual-level vcf files per sample. Where can I find joined called vcf files for WGS located? Please do let me know how to access those and use them for the extraction of the gene region I am interested in.?
- Former User of DNAx Community_6
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Will there be UKB WGS PLINK bfiles?
- Former User of DNAx Community_4
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Extract multiple regions from CRAM with samtools view on the RAP
- Permanently deleted user
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Are UKB pVCF wes files truly bgzipped?
- Former User of DNAx Community_22
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The sample code to load a VCF file with Hail is failing for me when I try it on a single 6 Gb VCF from the whole genome pVCFs. Can you help me to resolve this error?
- Former User of DNAx Community_47
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Hello, When looking at a specific variant in a cohort in the Genomics tab, is it possible have access to IDs of the patients having this specific variant ? Thank you !
- Former User of DNAx Community_74
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WGS cram files truncated?
- Permanently deleted user
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How to fix QCtool code to filter bgen file?
- Former User of DNAx Community_40
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dx error: unrecognized arguments for REGENIE
- Former User of DNAx Community_52
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Issue retrieving the data field 23196 ? Whole genome GATK joint call pVCF
- Former User of DNAx Community_30
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Whole genome GraphTyper joint call pVCF README with chromosome section specification
- Former User of DNAx Community_30
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Best resources for joint call pVCF exploration?
- Former User of DNAx Community_30
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Get EID of variant carriers from pVCF?
- Permanently deleted user
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How to import a VCF file? File not found error when importing VCF file with Hail
- Former User of DNAx Community_14
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can you match plink output to EIDs?
- Former User of DNAx Community_37
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Parallel analyses on WGS files
- Former User of DNAx Community_56
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Hello, 1) are the plink files for the WGS going to be available soon? 2) I need help to run batch jobs on SAK
- Former User of DNAx Community_56
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Hello, I am wondering if it's possible to input a script into swissarmyknife instead of individual commands? If so, how would I do this?
- Former User of DNAx Community_37
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Hello, If I am looking to create a dataframe of around 200,000 participants, with individual nucleotide information regarding around 20 SNPs, what is the best way to go about doing this? Thanks :)
- Former User of DNAx Community_37
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Hi folks, I have a basic question for you?how can we access the exome sequencing data (preferably as the VCFs) using HAIL on the UKB RAP?
- Former User of DNAx Community_7
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How to merge VCF files with Swiss Army Knife?
- Former User of DNAx Community_56
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Does anyone have a good tutorial on Eigensoft for use in DNAnexus?
- Former User of DNAx Community_33
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Best way to view a full VCF file?
- Permanently deleted user
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Is it possible to run Regenie step 2 with whole genome data rather than whole exome data considering that it is in pVCF format and there are more than 1 file for each chromosome?
- Permanently deleted user
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Best strategy for annotating and filtering VCF files using VEP on UKB RAP?
- Former User of DNAx Community_4
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For the WGS, where can I find a list of which samples were sequenced in each cohort (Sanger Main, Sanger Vanguard and deCODE)?
- Permanently deleted user
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Can you annotate with CADD, gnomad, clinvar and dbNSFP options when using hail on Spark jupyterlab notebooks?
- Former User of DNAx Community_4
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