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Hi,
what does the switch `-skipTriallelic` do exactly, i. e. how does ANGSD detect triallelic SNP's? Does it calculate L(D | ) or does it just discard all sites where three different bases are foun…
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Can I use realSFS specifying more than one region? if the answer is yes, how?
I am looking for the equivalent to -rf in ANGSD in NGSTools
The idea would be:
Estimate the SFS around SEVERAL R…
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ANGSD updated
6 years ago
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Hi there!
I would appreciate some help with installing ngsTools. After cloning latests version, running make and make tests, I get the following (on two completely different servers, CentOS 7.4.170…
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The docs mention `make && make test`
but the repo/examples/test.sh file refers to a folder `../../ngsSim` which I suppose is from a different repository.
where could i find the data ?
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I ran into this error
```
-----------------------------------------------------------------------
CAVA (Clinical Annotation of VAriants) v1.2.0 is now running.
Started: 2016-12-19 12:53:49.709035…
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Hi ANGSD team,
when running
>thetaStat do_stat out.thetas.gz -nChr 20
what does the number 20 stand for?
many thanks
claudius
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It's generally considered best practice to remove multimapping reads for ChIP-seq analysis (eg. the classic `bowtie -m 1` for bowtie1). Most modern mappers, including `bwa mem` that we use here, don't…
ewels updated
6 years ago
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Hello,
Using the 'git clone' option listed, we downloaded and attempted to install NGStools on our system (Linux, RHEL 6 x86_64), but the make seem to bail when it hit ANGSD, which we already have ins…
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Hello,
I try to reconstruct how sliding window calculation of FST by realSFS is done in ANGSD as i have to manually calculate sliding windows for subset of total sites in R.
normal output of F…