Whole Genome Sequencing

How to import a VCF file? File not found error when importing VCF file with Hail
- Former User of DNAx Community_14
- 19 August 2022 00:00
- 0 votes
- 13 comments
can you match plink output to EIDs?
- Former User of DNAx Community_37
- 16 August 2022 00:00
- 1 vote
- 1 comment
Parallel analyses on WGS files
- Former User of DNAx Community_56
- 16 August 2022 00:00
- 0 votes
- 2 comments
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
- 16 August 2022 00:00
- 0 votes
- 4 comments
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
- 12 August 2022 00:00
- 0 votes
- 1 comment
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
- 10 August 2022 00:00
- 0 votes
- 1 comment
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
- 10 August 2022 00:00
- 0 votes
- 4 comments
How to merge VCF files with Swiss Army Knife?
- Former User of DNAx Community_56
- 28 July 2022 00:00
- 0 votes
- 8 comments
Does anyone have a good tutorial on Eigensoft for use in DNAnexus?
- Former User of DNAx Community_33
- 13 July 2022 00:00
- 0 votes
- 5 comments
Best way to view a full VCF file?
- Permanently deleted user
- 05 July 2022 00:00
- 0 votes
- 1 comment
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
- 14 June 2022 00:00
- 0 votes
- 1 comment
Best strategy for annotating and filtering VCF files using VEP on UKB RAP?
- Former User of DNAx Community_4
- 10 June 2022 00:00
- 0 votes
- 1 comment
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
- 13 May 2022 00:00
- 0 votes
- 2 comments
Can you annotate with CADD, gnomad, clinvar and dbNSFP options when using hail on Spark jupyterlab notebooks?
- Former User of DNAx Community_4
- 06 May 2022 00:00
- 0 votes
- 2 comments
Cohort browser - Genomics - AF frequency and count not the same size as the cohort I built
- Former User of DNAx Community_39
- 24 April 2022 00:00
- 0 votes
- 2 comments
Is it expected that some WGS GraphTyper pVCF files have no variants?
- Permanently deleted user
- 07 April 2022 00:00
- 0 votes
- 6 comments
How can I identify which subjects have which alleles of rs56041637 in the WGS data? rs56041637 is an intron variant not in the imputed snps. https://www.ncbi.nlm.nih.gov/snp/rs56041637
- Former User of DNAx Community_10
- 05 April 2022 00:00
- 0 votes
- 8 comments
How do I load .p.vcf.gz files into the python environment on the spark cluster? Do I need to use dxdata?
- Former User of DNAx Community_4
- 01 April 2022 00:00
- 0 votes
- 3 comments
Hi, By whom and how were the helper filer for the 450K exomes generated? Has any filtering been applied for the pVCF or the plink files? Is the release on the RAP from this pipeline? https://www.nature.com/articles/s41586-021-04103-z
- Former User of DNAx Community_79
- 29 March 2022 00:00
- 0 votes
- 7 comments
I am wondering where I can find joint calling for whole genome data. For whole exome data there are 3 folders (population level exome OQFE variants) with joint calls in plink, bgen and pvcf format, but I don't see similar folder under whole genome data?
- Permanently deleted user
- 24 March 2022 00:00
- 0 votes
- 3 comments
How to use Ensembl Variant Effect Predictor(VEP) on UKB data for GWAS?
- Former User of DNAx Community_24
- 23 March 2022 00:00
- 0 votes
- 1 comment
Can I use GLnexus to create a pVCF for all of the females (273k people) in the UKB cohort?
- Former User of DNAx Community_32
- 22 March 2022 00:00
- 0 votes
- 4 comments
How can I run regenie step 2 for all 22 chromosomes at once? I would like regenie to spit out a single output file with gwas summary stats for all 22 chromosomes if feasible. Thanks
- Former User of DNAx Community_96
- 12 March 2022 00:00
- 0 votes
- 1 comment
cram cache download/internet access from samtools
- Permanently deleted user
- 27 February 2022 00:00
- 0 votes
- 4 comments
Are there alignment reports available?
- Permanently deleted user
- 24 February 2022 00:00
- 0 votes
- 4 comments
Are the unplaced contigs of Hg38 included in the alignments?
- Permanently deleted user
- 24 February 2022 00:00
- 0 votes
- 6 comments
Subsetting by genome
- Former User of DNAx Community_45
- 11 February 2022 00:00
- 0 votes
- 8 comments
Hi, can you give me an idea how to proceed with this; I have an existing series of perl scripts (a few thousand lines), to perform variant calling from cram files. Is there anyway I can translate my current approach onto the Dnanexus system? Thanks
- Former User of DNAx Community_80
- 10 February 2022 00:00
- 0 votes
- 7 comments
For pVCF files, e.g. GraphTyper SVs is there a list of the genomic positions of the first and last variant in each batch file ?
- Former User of DNAx Community_64
- 25 January 2022 00:00
- 0 votes
- 2 comments
Are there any examples of calculating the genetic risk score from different SNPs for a specific disease (e.g., diabetes) on the Research Analysis Platform (RAP)?
- Former User of DNAx Community_14
- 21 October 2021 00:00
- 0 votes
- 9 comments

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