User: Pablo
Pablo • 1.9k
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Posts by Pablo
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In my opinion, this sounds like a problem in the lift-over procedure, as opposed to a failure in the annotation software.
In order to correctly lift-over variants (e.g. a VCF file from ExAC), not only the coordinates should be changed, but also the variant's REF and ALT fields must be complemente ...
written 2.8 years ago by
Pablo • 1.9k
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... It depends in which format you retrieve the database. For instance, ClinVar is available in VCF and by definition VCF represents variants ok the plus strand, so there is no need to specify the strand (it is implied by the file format).
For what you are trying to achieve you don't need any of that. ...
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... I'm not sure what you mean by " heard some whispers recently saying that this tool wasn't up to date", but I'm developing SnpEff and the latest release was just a couple of days ago (and there have been new versions being released every couple of months since its inception).
The categories, which a ...
written 4.8 years ago by
Pablo • 1.9k
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... dbNSFP provides multiple values for those scores and SnpEff simply annotates them all.
The reason dbNSFP provides different values is related to how each score is calculated. For instance the number of PolyPhen entries usually the same as the number of Uniprot IDs, similarly the number of SIFT ent ...
written 4.8 years ago by
Pablo • 1.9k
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GRCh37.XX are form ENSEMBL genes. I'd recommend you use the latest one available (GRCh37.75).
...
written 4.9 years ago by
Pablo • 1.9k
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... If a VCF entry has two (or more) alts, SnpEff counts it as two (or more) SNPs.
For instance
CHR:1, POS:1234, REF:A, ALT:C
is 1 SNP (A>C) , whereas this entry
CHR:1, POS:1234, REF:A, ALT:C,G
is counted as 2 SNPs (A>C and A>G).
I don't know how freebayes counts, but I'm assumi ...
written 5.2 years ago by
Pablo • 1.9k
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If you are asking about programs and methods, a good starting point is "GATK's best practices":
https://www.broadinstitute.org/gatk/guide/best-practices
...
written 5.3 years ago by
Pablo • 1.9k
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... OK, my bad then. I'll try to delete / edit this answer. ...
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... It's weird that they mention KM034562 in the main paper, they asked me to provide "KJ660346" for their analysis...
...
written 5.3 years ago by
Pablo • 1.9k
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... Indeed. The question mentions "protein SNP analysis", so I'm assuming these are from sequencing data (otherwise it would be something like "protein polymorphism analysis"). May be sana can clarify a little bit more in the formats being used for the analysis... ...
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