Convert Bam To Bed/Fam/Bim

Question

[Anjali]

Hi,

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

Answer 1

[Aaronquinlan]

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.