svaba

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Is it possible to infer duplications/deletions/translocations/insertions/inversions from SvABA output?

2

Hi, I have a series of SvABA vcfs, and I wanted to know if it was possible to tell somehow the type of a variant, since the field "TYPE" has...

Giuseppe1995

"Duplicate" kgID when doing annotation.

2

I am trying to running the annotation (svaba-annotate.R) on GENCODE db. However, the UCSC db records pulled by these 2 lines. https://github.com/walaj/svaba/blob/0f60e366c300bbefbba762bcc6d2b661bd2ae74a/R/svaba-annotate.R#L59-L60 Are having duplicates. example: ``` kgID mRNA geneSymbol...

sxwcasd

pretty simple. -t works --case-bam does not

aubreybailey

Specific types of BND

2

Hi, could you please provide a script for converting BND svtype to specific SV types, e.g. DEL, DUP. I don't think the one in #4 is accurate. Thanks,

hurleyLi

Hi, Since variant types are specified in BND formats. How can I extract each variant type? Would it be possible to give me an example of extraction of deletions from...

Danisov

Recommendation of QUAL?

2

Hi, does QUAL here has the same meaning as QUAL in SNV calling, and is there any specific recommended threshold of QUAL for filtering low quality SVs called by SvABA?

greekkey

Hi, (1) Are there any parameters can be used to change the threshold for the length of SV and indel events? (2) If I want to extract all variants in...

tgong1

ERROR: Unable to open index file: ucsc.hg19.fa, yet it's in the current directory.

2

bash-4.2$ /data/CCRBioinfo/dalgleishjl/sv_mapping/svaba/bin/svaba run -t PAMHYN_Tumor.realigned.md.bam -n PAMHYN_Normal.realigned.md.bam -a PAMHYN_discovery_chr22 -k chr22 -G ucsc.hg19.fa -p 2 ----------------------------------------------------------- --- Running svaba SV and indel detection on 2 threads ---- --- (inspect *.log...

jamesdalg

Hello, I am wondering if there is a plan to modify SvABA to allow analyzing non-paired, long read sequences such as Oxford Nanopore data. Or I am wondering if if...

ehjChun

Hello, I have two questions about *alignments.txt.gz: 1. As an example, I wonder how the following text should be interpreted. Does it mean there is a breakpoint between 1:1,363,501 and...

yifnzhao