characterizer excision problem

[jacau]

Hi,

I'm using relocate2 and then characterizer for genotype calling and excision. The genotype calling is working fine, however there is an issue with the excision determination. I'm getting this error message:

[E::mpileup] fail to parse region 'S4:S4.13954589' with /ohta/jasmina.uzunovic/S4.13954589.sorted.bam [afs] 0:0.000

Do you know what the problem might be? Could it be a samtools version incompatibility? I'm currently running it with the newest version (1.3).

[srobb1]

Hi Jacau,

I have not used RelocaTE in a while. My old lab has forked this repo. Try using RelocaTE from the Stajich Lab (https://github.com/stajichlab/RelocaTE2). Let me know if this bug is still an issue, I will happily dive in figure it out.

Sofia

[jacau]

So I have been using RelocaTE2 from the link you sent, however the documentation for characterizer.pl links back to this page (and I don't think it's been altered for RelocaTE2).

I did notice one samtools incompatibility, in some previous version you could call 'samtools sort sample.bam sample.sorted' but now you have to call 'samtools sort sample.bam > sample.sorted.bam', and I changed this in the script, but then I get the error where the script calls samtools mpileup (the error I posted above). I've also never coded in perl, making it a bit trickier to figure out what the exact issue is (whether it's a samtools incompatibility or something else).

I'd really appreciate any help, thanks!

[JinfengChen]

Hi Jacau,

I think that might be a samtools version problem. I will test the script. Can you list your command line that gives errors. It will help me to find the problems. Thanks a lot.

Jinfeng

[JinfengChen]

I did not use excision option at all. So I think I never tested or changed that part. If you want to try some testing before I get back to you. You can use samtools 0.1.19 and use the script from this repository.

Jinfeng

[jacau]

Thanks Sofia and Jinfeng.

I ran with the command line: RelocaTE2/scripts/characterizer.pl -s 16_70X_bow/repeat/results/ALL.all_nonref_insert.txt -b bam_files/16_70X.sorted.bam -g C_rubella_ref_files/C_rubella_ref_S8 -x 1 --samtools samtools --bedtools bedtools &

I tried running with samtools version 0.1.19, however that still gives me errors:

[sam_header_read2] 8 sequences loaded. [bam_parse_region] fail to determine the sequence name. [mpileup] malformatted region or wrong seqname for /ohta/jasmina.uzunovic/S1.4637121.sorted.bam [afs] 0:0.000

[JinfengChen]

I made the script to run. Please check the version at https://github.com/stajichlab/RelocaTE2. I tested on samtools 0.1.19. It also need bcftools. I like to specify the path of tools by options but also works if they are in $PATH.

According to the descriptions in the G3 paper, I think the excision result may include only somatic excision. Please check the result if that works for you. Thanks for using RelocaTE/RelocaTE2.

Jinfeng

[srobb1]

Thank you Jinfeng!!!!

Yes, let us know if this does not work.

Sofia

On Sun, Dec 18, 2016 at 6:21 PM, JinfengChen notifications@github.com wrote:

I made the script to run. Please check the version at https://github.com/stajichlab/RelocaTE2. I tested on samtools 0.1.19. It also need bcftools. I like to specify the path of tools by options but also works if they are in $PATH.

According to the descriptions in the G3 paper, I think the excision result may include only somatic excision. Please check the result if that works for you. Thanks for using RelocaTE/RelocaTE2.

Jinfeng

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/srobb1/RelocaTE/issues/5#issuecomment-267862389, or mute the thread https://github.com/notifications/unsubscribe-auth/ABBfX7wj22K187dkAA0YOjTc4ymSf5yVks5rJdwMgaJpZM4LOuK- .

[jacau]

Thanks to both of you! Works great now! :)

Jasmina

[JinfengChen]

Great! Good News before the holiday. Merry Christmas and happy new year

Jinfeng

[srobb1]

Yeah!