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I am trying to run demuxlet on a big vcf file (~500Gb); but I am getting the following error that can be due to the memory running out the error (?), can you please suggest how can I get rid of it?
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In your vignette you state that: "Pre-computed [marker maps] for the MUGA series of arrays are available from [URL]."
What is the URL for downloading the marker map file?
Thanks!
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您好!基于图形泛基因组,采用vg软件call程序,获得了2000多个个体vcf文件需要合并,对于survivor软件,使用./SURVIVOR merge sample_files 1000 2 1 1 0 30 sample_merged.vcf;对于panpop软件,请问是否使用./subworkflows/mergeSV3_pop.py脚本合并就可以?不需要额外执行./bin/PART_ru…
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### # Downloads input files:
### #Known variant file
`[wget ftp://ftp.ensembl.org/pub/release-99/variation/gvf/homo_sapiens/homo_sapiens-chr18.gvf.gz' -O homo_sapiens.vcf.gz](url)`
# # Select varia…
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Slack: https://centrepopgen.slack.com/archives/C018KFBCR1C/p1714624645731339
## TL; DR
We're shoving a lot of stuff into analysis entry `meta`, and it's making metamist really unhappy
### Hef…
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**1. What were you trying to do?**
I would like to convert haplotype sampled GBZ graph to GFA, with GRCh38 path written as rGFA tags.
**2. What did you want to happen?**
Generate an GFA f…
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I'd like to read in plink data to `int8` arrays rather than `float32`. Looking at `_bed_read.py` it seems this could be done at the chunk level by modifying `_read_bed_chunk()`. Are their any gotchas…
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I have a question regarding the first imputation step using Beagle. My experience with imputation is strictly from a GWAS perspective where imputation from a large DNA array panel will result in the …
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I've noticed that missing data in my merged vcf file following genotyping are haploid ".:" while all genotypes with data are correctly diploid. Running the` sed -e 's/ \.\:/ \.\/\.\:/g' `line…
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Hi!
I'm running variant calling on a batch of 80 bovine WGS samples and the workflow is failing at the SV stage with Manta. I've previously tested it on 2 samples and that worked fine.
This is t…