BED file format - FAQ

UCSC very good description of the BED format
http://genome.ucsc.edu/FAQ/FAQformat.html#format1



Bedtools attempts to auto-detect the file formats used in each command.  Thus, as long as your file conform to the format definitions for each file type, you should be okay.  For example:

- BAM is zero-based, half-open.  SAM is 1-based, closed.
- BED is zero-based, half-open.

zero length intervals (start == end), which in BED format, are interpreted as insertions in the reference.

I can't confirm this but from the top of my head, I recall that

start -1, end in BED format refers to SNPs


(source mostly from BEDTools mailling list)

Convert SAM / BAM to fasta / fastq

Probably one of the most freq FAQ

latest thread in biostar
http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file

Samtofastq using Picard
http://picard.sourceforge.net/command-line-overview.shtml#SamToFastq

Samtools and awk to make fasta from sam

samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > filename.fasta

Biopython and pysam (code contributed by Brad Chapman)

http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file/6994#6994