Question: Merging individual .bed files?
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gravatar for genomics Newbie
4 months ago by
genomics Newbie10 wrote:

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.

.bamtobed samtools .bed .bam • 246 views
ADD COMMENTlink written 4 months ago by genomics Newbie10
1

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

ADD REPLYlink written 4 months ago by goodez390

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

ADD REPLYlink written 4 months ago by steve1.8k

SNP genotype analysis

ADD REPLYlink written 4 months ago by genomics Newbie10
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