Discovering chromosome name in snpEff database
Hey dear biostars,
I wonder how can I find out how to discover the name of the chromosome in the snpeff database from it bin file?
Thank you
snpeff
• 856 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
ziziqolo •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
written by ekirsch •Hello BioStars Community, I have been encountering an issue with SnpEff where it assumes circular chromosomes during the annotation of a eukaryotic genome (Savannah Sparrow), …
-
snpEff: ERROR_CHROMOSOME_NOT_FOUND
written by ziziqolo •Hey BioStars I'm trying to annotate my bacteria variants with SnpEff, java -jar snpEff.jar -v Mycoplasma_hyopneumoniae_168_l /mnt/f/mycopn/variantcalling.vcf > /mnt/f/mycopn/res.ann.vcf All my Reference and snpEff database …
-
Construction of the reference genome database (GCA_000001405.15_GRCh38) with snpeff
written by Adham •Dear colleagues I used the reference genome GRCh38 version GCA_000001405.15_GRCh38 / seqs_for_alignment_pipelines.ucsc_ids downloaded from [https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/][1] This version was used for alignment and variant calling, however, …
-
snpEff ERROR_CHROMOSOME_NOT_FOUND GRCh37.75 genome
written by rbioinfo •Dear Biostar community, I have a targeted resequencing experiment (Illumina) with the goal to detect mutations in certain genes. For this purpose, to align reads, …
-
Cancer Cell Line WGS
written by denis.k •Hey Biostars! Was wondering if someone could help me out with this problem. I am looking for WGS data from cancer cell lines but have …
-
How to use wheat chromosome 3D as input for snpEff?How I can add the wheat reference genome databas…
written by pltbiotech_tkarthiHow I can add the wheat reference genome database (I need to install 3D chromosome based database for the annotation of VCF file from 3D …
-
Identify or update refseq transcript version on snpeff
written by NBHello, I am using snpeff version 4.3t and have downloaded the database for hg19 to annotate my vcf files. However, the refseq version number of …
-
SNP annotation using gff3
written by rezahi everyone i am trying to annotate of identified SNPs and INDELs (vcf format) using software such as snpEff. i downloaded gff3 file correspond to …
-
Extract PDB file names from KEGG when Gene name is known
written by DanielCDear All, I am looking for a **standalone** way to extract pdbs from KEGG when I have the gene name. For instance, I know "HRAS" …
-
External hard drive BLASTDB path not recognized
written by JenezHi there! Hopefully this does not stray too far away from the bioinformatical side of the site... Question: I'm saving my local blast databases on …
it looks like the names of the chromosome are in the bin filename. Here is my directory for human: