Merging individual .bed files?

Question

[genomics Newbie]

Hello,

Our main goal is to create a single set of .bed/.bim/.fam files from our .bam formatted sequences. However I’m finding that merging, sorting and indexing these .bam files (appox. 100) via samtools is exceeding our processing and storage capabilities.

1). Is there any other means by which we could create the .bed files without having to initially merge each .bam file?

2). Is it possible to create an individual .bed file using bamtobed tools for each .bam file and then merge these .bed files?

3). Does .bamtobed also create the .fam and .bim files?

Thank you.

[goodez]

2). Is it possible to create an individual .bed file using bamtobed tools for each .bam file and then merge these .bed files?

Yes. You can make individual BED files from each BAM. Then merge the BED files using a tool like bedtools merge

[steve]

for what kind of purposes were you planning to use this merged file?

[genomics Newbie]

SNP genotype analysis