samtools-1.1 rmdup error

Question

[hellbio]

Hi all,

I have recently upgraded to the recent version of samtools-1.1. Using 'rmdup' with samtools produces the below error:

"Samtools-htslib-API: bam_get_library() not yet implemented"

Could anyone help to fix this?

[Devon Ryan]

Thanks for mentioning this on the samtools list as well! Hopefully that'll finally push someone to write bam_get_library() (in fact, maybe I'll have time tonight...we'll see).

Answer 1

[NB]

I had this problem before, this is a known bug in samtools > 1.0 ...see e.g. https://biostar.usegalaxy.org/p/7928/ and https://biostar.usegalaxy.org/p/9335/... What I did was to just install samtools < 1 and it was okay then.. maybe you can give that a try?

[hellbio]

thanks!! samtools < 1 works perfect.

[Prakki Rama]

I installed samtools < 1. It worked for me too.

Answer 2

[ATpoint]

I encountered the same error with samtools-1.2 but not with the current samtools-1.3. In 1.3 it works fine for me with:

• rmdup -s singleend_input.bam singleend_output.bam
• rmdup pairedend_input pairedend_output

Don't forget to sort your files prior to rmdup.