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Ideally, this would automatically update priors too, somehow...?
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Hello Robert,
Is there a way to output the estimated recombination rate positions?
Thanks
a
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Hi,
toil-vg crashed again on the cactus graph of yeast genomes. I was able to reproduce the issue on my laptop with v1.11.0-74-gdab42acd:
```
>vg call chunk_Y12.chrIII_0_aug.vg -t 1 -S SRR40743…
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```sh
$ cat _Recal_Patient157.err
R scripting front-end version 3.4.2 (2017-09-28)
##### ERROR ------------------------------------------------------------------------------------------
##### ERRO…
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Hi,
Previously I posted a couple of times, struggling to make DNG work on my VCF file of a trio dataset, but could not get any result. If someone has a working example, where de-novo mutations c…
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Hello, I'm having a problem using your program with my data.
My data consists of 14 samples that were sequenced low-coverage (Ion Proton). The mean coverage for these sample is around 0.8-1.2.
Beca…
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What SNP callers do you recommend for making vcf?
`library(GUSMap)`
`RAfile filter$DEPTH) { :
missing value where TRUE/FALSE needed
We usually use two SNP calling methods to make vcf files,…
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I am using SV2 on a large cohort (300 samples). In my current Delly2 pipeline, I create "cross cohort" VCF files, i.e.
- call variants in all samples
- merge variant files into a "cohort variation…
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@vdauwera commented on [Wed Mar 22 2017](https://github.com/broadinstitute/gatk-protected/issues/950)
@vruano commented on [Wed May 18 2016](https://github.com/broadinstitute/gsa-unstable/issues/1376…
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Importing sample1:
```
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1
chr20 1274366 . A G, 562.77 . DP=26;MQRankSum=-1.011;MQ_DP=26;QUALapp…