Carefully opt for human reference genome

biogeek — Tue, 18 Feb 2020 07:43:32 -0600

Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.

if you map reads to GRCh38 or hg38, use the following:

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:

More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Address of the bookmark: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Converting a VCF into a FASTA given some reference !

Jit — Fri, 20 Jul 2018 10:03:53 -0500

Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

BOL: Related items

Carefully opt for human reference genome

Converting a VCF into a FASTA given some reference !