User: bgold04

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bgold040
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Posts by bgold04

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Answer: A: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
... I did this using Wouter DeCoster's suggestion, something like: vcftools --vcf my.vcf --recode --keep-INFO-all --exclude-positions All_20160408.bed It were not pretty making the bed file, and I worry that, because I am excluding by position rather than genotype [eg. A/T at rsXXXXX], I may exclude ...
written 13 months ago by bgold040
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bcftools filter or bcftools isec to EXCLUDE dbSNP snps
... I am not a newbie but I am having a brain block. I want to exclude dbSNP snps from a vcf file. Don't ask me why. Anyhow if A.vcf.gz is my vcf file and All_20160408.vcf.gz is the dbSNP vcf file, what do I do? [stupid suggestion to show I am trying....: bcftools filter -e (All_20160408.vcf.gz) A.v ...
filter bcftools vcftools isec dbsnp written 13 months ago by bgold040 • updated 13 months ago by harold.smith.tarheel3.9k
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Comment: C: Amino Acid Change To Genomic Location: using 'backlocate'
...     I tried compiling jvarkit and got the following error (only last ~25 lines reproduced below), the make then quit. htsjdk-jar: [mkdir] Created dir: /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist [jar] Building jar: /Users/bertgold/Documents/jvarkit/htsjdk-1.139/dist/htsjdk-1.13 ...
written 2.0 years ago by bgold040
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Requesting help building a bacterial database file consistent with gibVirus.fa
...   Biostars, The genome information broker for viruses (gibVirus) contains a .fasta file with over 18,000 full length viral genomes ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781101/ ).  This is useful for viral detection and providing integration boundaries using a perl script developed under ...
wget ftp bacteria mget viruses written 2.9 years ago by bgold040 • updated 2.7 years ago by Biostar ♦♦ 20

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