Comments (1)
ctokheim
commented on June 2, 2024
Hi. The snvboxGenes.fa file (i.e. input of -i in mut_annotate) is generated from the extract_gene_seq command (see https://probabilistic2020.readthedocs.io/en/latest/tutorial.html#gene-fasta). One just needs to download the hg19 fasta file from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit), convert the file from 2bit to fasta format using the twoBitToFa command line tool from UCSC, and then run extract_gene_seq command with hg19.fa and snvboxGenes.bed as input.
I've also attached the snvboxGenes.fa file below as well.
snvboxGenes.fa.gz
from 2020plus.
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