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How to extract and save the header of .bam,vcf and idat files in a text file

Can someone help with how to extract the header data (metainfo) from these three files: .bam, vcf and idat files.

I want to be able to extract these medatadata info and save each in a text file. I hope someone can help me with the how to.

Thanks!

bam ida vcf extract header
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updated by Giulio Genovese • Giulio Genovese • written by nsonkole • nsonkole

2 answers 

## BAM:
samtools view -H file.bam > header_BAM.txt

## VCF:
awk '{if(/^#/)print;else exit}' file.vcf > header_VCF.txt

For idat I don't know.

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written by ATpoint ATpoint

You can use my bcftools plugin gtc2vcf as follows:

bcftools +gtc2vcf --idat file.idat

There is header information both at the beginning and the end of an IDAT file though

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written by Giulio Genovese • Giulio Genovese

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