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arundurvasula / angsd-wrapper

A project for extending ANGSD
MIT License
8 stars 12 forks source link

Header Requirements #86

Closed mojaveazure closed 9 years ago

mojaveazure commented 9 years ago

The current version of SAMtools is no longer creating headers. Using their dataset, I have run:

samtools view -bS toy.sam | sort - toy samtools view -bT toy.fa toy.sam | sort - toy

to create sorted bam files. Each time, I get the following bam file samtools view -H toy.bam | head

@SQ SN:ref LN:45 @SQ SN:ref2 LN:40

Can the requirement for headers starting with @HD be removed? Surely there's a way to find specific regions without @HD headers.

arundurvasula commented 9 years ago

I don't think we can do this with angsd-wrapper but it may be possible to add it to ANGSD? Try: https://github.com/angsd/angsd