bam to vcf to .bed

Question

[genomics Newbie]

Is the following the correct process? I do not believe I can "convert" .bam to .bed directly. I am converting .bam to vcf using bcftools, and then using plink to prepare .bed and .fam files.

bed to vcf using bcftools

vcf to bed using plink

bed + fam using plink

Thank you.

[Ram]

I think you're using the word "convert" a little incorrectly here. One cannot "convert" a BAM to a VCF because they do not represent the same information. You can obtain a VCF by processing a BAM with a (reference) FASTA, but cannot convert the BAM to a VCF. You can also extract a BED out of a VCF, but you don't convert it there either. I'd only use "convert" if the information content in the formats is comparable tending to equivalence.

[Medhat]

You can convert from bam2bed directly http://bedtools.readthedocs.io/en/latest/content/tools/bamtobed.html

Maybe you can elaborate more why you are first convert to vcf?

[swbarnes2]

What do you want your bed file to contain? Coordinates of variants? Coordinates of mapped reads?

[GenoMax]

genomics Newbie : Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they all work.

Please do the same for your previous posts as well.

Answer 1

[WouterDeCoster]

Important: there are two types of bed files containing entirety different information. The type you want (plink) is not the same as mentioned in the other comments. What you are doing is fine.