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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…
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Merging the variants of the same sample from 2 different variant callers, namely DELLY and MANTA, is generating no collapsed variants.
I ran
`bcftools merge -m none --force-samples delly.vcf.gz m…
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Hi,
Thanks for developing this awesome tool.
I'd like to call somatic structural variants (SVs) using paired tumor and normal samples. However, cuteSV can only process one sample at a time.
I…
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I'm interested in tracing previously identified somatic mutation for each single cell. am wondering if the souporcell_merged_sorted_vcf.vcf.gz contains only germline variants or it also contains somat…
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Hello, I'm having issues to update the main header in the html table when I pass custom info-columns information:
create_report test.bed --genome hg38 --fasta hg38.fasta --info-columns CHROM START …
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Hi,
I'm experimenting with running COMPASS (using CNVs) with multiple samples (3 samples), where the cells then come from different runs with MissionBio. A problem is that they got sequenced at dif…
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### Need
As a geneticist I want to see true variants and not false positive calls. Currently we have databases for annotating variants that are commonly observed as somatic in highly filtered T+N c…
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we will need to disambiguate between variants (and perhaps any geno partonomy) that are germline vs somatic.
how should these be represented? should there be classes for "germline variant" "somati…
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Hello,
I am aware that this question has been asked before, but still I (and others, when looking around in recent posts on Biostars and Seqanswers) have trouble with properly filtering somatic var…
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### Submitter Name
Grace Pendlebury
### Submitter Affiliation
Shariant / Australian Genomics
### Submitter Github Handle
_No response_
### Additional Submitter Details
Shariant is…