Question: bam to vcf to .bed
gravatar for genomics Newbie
7 months ago by
genomics Newbie20 wrote:

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.

bam bed vcf • 357 views
ADD COMMENTlink modified 7 months ago by finswimmer9.9k • written 7 months ago by genomics Newbie20

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.

ADD REPLYlink written 7 months ago by RamRS20k

You can convert from bam2bed directly

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

ADD REPLYlink modified 7 months ago • written 7 months ago by Medhat8.1k

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

ADD REPLYlink modified 7 months ago • written 7 months ago by swbarnes24.8k

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.

ADD REPLYlink written 7 months ago by genomax62k
gravatar for WouterDeCoster
7 months ago by
WouterDeCoster36k wrote:

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.

ADD COMMENTlink written 7 months ago by WouterDeCoster36k
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