Question: Convert Bam To Bed/Fam/Bim
gravatar for Anjali
8.7 years ago by
Anjali60 wrote:


I used Bedtools to convert BAM to BED format for my sequencing data. But together with BED I need the corresponding BIM and FAM files, which are not generated automatically by it. Now, I work with PLINK which has an option to convert such files but the input file should be PED and I couldnt find anyway to convert BAM to PED. It would be really helpful if anyone can suggest me a way for conversion of BAM to BED/BIM/FAM files.

Thank you

bed bam conversion format • 5.3k views
ADD COMMENTlink modified 8.4 years ago by Aaronquinlan11k • written 8.7 years ago by Anjali60
gravatar for Aaronquinlan
8.7 years ago by
United States
Aaronquinlan11k wrote:

I think you need to read up on what the BIM and FAM formats are to understand why you cannot go directly from BAM to those formats. You should use a variant calling algorithm (e.g. GATK or FreeBayes) to produce a VCF file from your BAM file. After this, you could use PLINK-SEQ to convert the VCF file to the standard PLINK formats such as MAP/BIM and FAM.

In short, the BAM format (and VCF for that matter) have insufficient information from which to create complete BIM/FAM files.

ADD COMMENTlink written 8.7 years ago by Aaronquinlan11k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1112 users visited in the last hour