Question

How To Convert Bam To Ped/Map File

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13.9 years ago

Anjali ▴ 60

Can anyone suggest me how to convert a BAM allignment file to a PED and a MAP file format??

Thank you

conversion • 5.6k views

ADD COMMENT • link updated 13.9 years ago by Sean Davis 27k • written 13.9 years ago by Anjali ▴ 60

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Your previous thread asked the same question.

ADD REPLY • link 13.9 years ago by Zev.Kronenberg 12k

Ram · Answer 1 · 2011-12-20

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13.9 years ago

Sean Davis 27k

BAM is an alignment format and does not describe genotypes. You will need to call genotypes on your samples using a tool such as samtools mpileup. The output from that will be VCF format. From the answer to your other related question,

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ADD COMMENT • link updated 6.1 years ago by Ram 45k • written 13.9 years ago by Sean Davis 27k