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my command is:
`$VEP/vep --fork 8 --refseq --use_given_ref --force_overwrite --coding_only -i $IN/$BASE.vcf -o $OUT/$BASE/$BASE.csv --cache --offline --refseq --format id --assembly GRCh37 --tab --ch…
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I'm encountering a segfault while training on the Toronto Book Corpus.
For training I'm using:
`./fasttext sent2vec -input ../input.txt -output my_model -minCount 5 -dim 700 -epoch 12 -lr 0.2 -wordN…
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In a two-ancestry scenario, one of the ancestral population (`-p 0`) may contribute more than one pulse at different times. To estimate this, I specified multiple pulse introgressions from that popula…
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I'm recently running PVACseq on a bunch of VEP-annotated germline variants vcf with netMHC, and some of the samples will show up an error of "Type names and field names must be valid identifiers" in C…
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I recently updated software to samtools/bcftools-1.8 (from v 1.2). After mapping of illumina data to a references (using BWA), I use samtools to call SNPs and bcftools to produce VCF files.
While …
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For sample.vcf, these two metrics are identical. Seems like there's a problem somewhere.
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This is somewhat similar to previous issues so I hope it's a quick fix.
It's the pipeline update time of year, and I think this issue is being caused by SpliceAI. Essentially, SpliceAI is adding mu…
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Hello!
While using smc++ for my inbreeding species, I stumbled across an interesting problem. The selection of distinguished pairs usually falls for two "chromosomes" of a single individual. Unfort…
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- Emacs package: elpy 20160903.841
- Python package: elpy-1.12.0.dist-info
I use the rope backend.
With `(elpy-use-ipython)`: when I open a Python file for the first time, I get the following error …
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I have successfully annotated my vcf file using a local installation of variant effect predictor (VEP). However, the filtering doesn't work. E.g. the command
`filter_vep -i vep.test.vcf.gz -filter …
matmu updated
5 years ago