This is a test version of Biostars. For the public version, visit https://www.biostars.org.
samtools view sample.bam >sample2.sam : lost the header

First , 

samtools view -Sb sample.sam >sample.bam

Second,

samtools view sample.bam >sample2.sam

I used this method: sam2bam2sam found that the head of the original sam file was lost at the end. So was it lost in sam2bam or bam2sam?

ps：sample.sam have header information，sample2.sam don't have header information.

samtools
• 2,496 views • link
updated by finswimmer finswimmer • written by flystar233 • flystar233

2 answers

samtools view -h sample.bam > sample.sam

• 0 views • link
written by Devon Ryan Devon Ryan

You must use the -h parameter when converting from bam to sam.

But why are you doing this?

• 0 views • link
written by finswimmer finswimmer

Log in to answer this question.

More posts like this