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Hi,
The link to angsd is broken.
I used this repo : https://github.com/ANGSD/angsd
And processed as mentionned in the README.
git clone https://github.com/samtools/htslib.git;
git clone https://gi…
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If we have a region in which some samples do not have coverage (e.g. due to presence/absence variation), how will ANGSD handle this? Will it calculate diversity given the samples it has coverage for? …
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I am having trouble getting ngsCovar to play nice with the 2D SFS from the recent version of ANGSD.
As mentioned, I am trying to use a 2D SFS from the new ANGSD output because it is quite simple to g…
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Hi Filipe,
I wonder if you could help solve compile problems of ngsDist. On a cluster running CentOS release 6.5 (Final) with gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) I get the following e…
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I ran oncotator on a HC called VCF using the command
oncotator -i VCF -o VCF --db-dir /path_to/ngstools/oncotator_v1_ds_Jan262014/ Project_bwa_GatkHC.vcf Project_bwa_GatkHC_oncotator.vcf hg19
The sc…
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script to run through ngsF from ngstools. TVK working on initial version. Should ideally output file of values for use in thetas etc. scripts.
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https://github.com/mfumagalli/ngsTools
First priority is ngsPopGen.
Later, can change to include entire ngsTools repository.
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Hello,
I was rellay happy to see ngstool working in combnation wit ANGSD. I made my first steps with ANGSt recently , and tested ngsF. I am working n yeast and I was interested in estimating selfing …
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After running a set of BAM files from multiple individuals through ANGSD, I'd like to take a closer look at summary statistics calculated by ANGSD for a single (inbred) individual BAM to assess some p…
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Howdy, and thanks for putting this on github, I'm a fan. Appears you've been rewriting commit history, which causes merge conflicts when I try to git pull to get newest changes to code. See http://g…