To make a genome file (for bed tools) using reference genome

1) Use samtools to generate fasta index samtools faidx lyrata_genome.fa - this will create a lyrata_genome.fa.fai (index file)

But, this index file won't work as genome file due to file format issue (mainly more than required number of columns).

2) take the index file, then use awk

awk -v OFS='\t' {'print $1,$2'} lyrata_genome.fa.fai > lyrata_genomeFile.txt

• this prints the 1st and 2nd column of a fai index file and separates the column by tab (OFS flag).
• use this file as genome file in bedtools.

if space desired between columns do this

awk {'print $1,"",$2'} lyrata_genome.fa.fai > lyrata_genomeFile.txt

if 'chr' needs to be added infront of the chromosome/scaffold names do this

awk {'print "chr"$1,"",$2'} lyrata_genome.fa.fai > lyrata_genomeFile.txt

If you are referring to the '-g' flag you can simply use the 'fetchChromSizes' script (link is to a 64bit Linux binary).

fetchChromSizes hg19 > hg19.chrom.sizes

'hg19' is an example, but any of the other UCSC genomes can be used, e.g. mm9, sacCer3, etc.

The '>' is a redirect to a new file.

The output is a tab-delimited file of chromosome name followed by it length.

I hope that helps.

This is too old , but I just saw it :)

you can use this with the bam file itself if it has the header:

samtools view -H my.bam | grep -P '^@SQ' | cut -f 2,3 | awk 'BEGIN{OFS="\t"}{split($1, a, ":"); split($2, b, ":"); print a[2], b[2] }'

I think this answer might be helpful although I am late. I saw this from the help page of genomeCoverageBed:

Tips:
One can use the UCSC Genome Browser's MySQL database to extract
chromosome sizes. For example, H. sapiens:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
"select chrom, size from hg19.chromInfo" > hg19.genome

samtools faidx output is pretty much what a genome file looks like. So run that on your reference genome.