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Hello,
Thanks for the package it is very useful and i was able to use it correctly but I haven’t included the use of structural variants (for plotting, since it is not used for calculations).
Could …
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Hi,
Thanks for developing this nice tool.
I have two genomes, assembly1 and assembly2. My goal is to use these two genomes as reference genomes, align reads to each of them, and call variants. T…
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http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/VCF%20(Variant%20Call%20Format)%20version%204.0/encoding-structural-variants
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Currently we assume that every variant is a focal change with a nucleotide `alt` sequence. This is only a subset of the VCF spec and doesn't allow us to load variants such as:
```
#CHROM POS ID RE…
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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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Hello,
Does LDSC analyze structural variants, such as deletion, inversion?
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Hi i am running mity via docker but encountered with some bam error, could not able to rectify it, actually i was trying to find out INDELS for long read ONT generated data, using minimap2 aligned bam…
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It should be possible to supply a VCF file of structural variants for each sample. If nothing is given, the workflow should behave as it is at the moment, otherwise the structural variants should be a…
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Hi, i am using the following command for mity INDELS finding using ONT generated data, which has been aligned by minimap2 aligner. Here i am using a single BAM file as a input. i am a bit confuse to t…
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Hello ,
I am trying to run structural variants annotations using annovar. Do annovar support it? If so can u help me with how to toggle structural variants input so the algorithm can get that?
R…