Question: samtools-1.1 rmdup error
2
gravatar for hellbio
4.7 years ago by
hellbio370
hellbio370 wrote:

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?

rmdup samtools • 4.8k views
ADD COMMENTlink modified 3.2 years ago by ATpoint19k • written 4.7 years ago by hellbio370

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).

ADD REPLYlink written 4.7 years ago by Devon Ryan91k
1
gravatar for Nandini
4.7 years ago by
Nandini820
London
Nandini820 wrote:

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 ?

ADD COMMENTlink written 4.7 years ago by Nandini820
1

thanks!! samtools < 1 works perfect.

ADD REPLYlink written 4.7 years ago by hellbio370

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

ADD REPLYlink written 3.2 years ago by Prakki Rama2.3k
0
gravatar for ATpoint
3.2 years ago by
ATpoint19k
Germany
ATpoint19k wrote:

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.

ADD COMMENTlink written 3.2 years ago by ATpoint19k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 701 users visited in the last hour