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Hi,
i ran whatshap v1.3 on pacbio aligned bam and vcf (deepvariant snv and sniffle sv, combined into one vcf) with
`whatshap phase -o svcall/$id.phased.vcf.gz --reference T2T-CHM13v2.0_genomic_ch…
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Hey guys, thx for the great tool!
I was just wondering whether I have missed something or is there just not more documentation on the output files available?
My specific questions:
1. **event_a…
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When listing genes included in structural variants what is the order the genes are listed? would it be possible to keep the genomic order instead? this will be much more useful specifically to be able…
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Thank you for an excellent and well-documented resource.
According to the catalogue
"Before insertion into GenPhenSQL, all variant coordinates were normalized with bcftools norm; variants that
…
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Should we require that a 'transcript-level' variant as the subject for this annotation type (and perhaps other VA types)?
Some data sources will enforce this and provide only transcript-level va…
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I've just read about [The Matched Annotation from the NCBI and EBI](http://www.ensembl.info/2018/10/12/our-new-joint-transcript-initiative-the-matched-annotation-from-the-ncbi-and-ebi-mane-project/) p…
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(I reckon that's clearer and more consistent with the dialog box description "Filters can be used to show only the rows that meet specific criteria.")
HOME [tab] > Explore genomic data through the V…
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This `variant-overlap` program was original designed for use with SNP's, which have simple coordinates, but structural variants have more complicated genomic coordinates and representations in .vcf/ma…
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The [Variant Interpretation for Cancer Consortium](https://cancervariants.org) is a data integrator that works to standardize and integrate content of knowledgebases of clinical interpretations for ge…
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I used VarTrix to extract single cell variant information from our 10x Genomics single cell data
$vartrix --bam $out_bam --cell-barcodes $barcodes --fasta $fasta_file --vcf $out_vcf --out-variants $o…