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What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
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Using `bedops --intersect` and `gtf2bed` will get their common genomic space:
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```bash
# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile
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> System Information: Ubuntu 22.04 (WSL2)
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> Shell: zsh
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Did it affect the bamtofastq output file? if so how did you solve the problem?
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You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
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0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
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Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
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Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
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> My problem has been with trying to loop the process.
ok here is a **nextflow** based solution,(NOT tested)
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I see.
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bedtools intersect \
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I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
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