Question: Realigner Target Creator in GATKtools
1
gravatar for mltlbrt
4.1 years ago by
mltlbrt10
United States
mltlbrt10 wrote:

Hi,

I am attempting to realign with Realigner Target Creator in GATKtools. However, when I upload the BAM file, I keep getting the message, "Sequences are not currently available for the specified build". Also the reference genome dropdown tab says, "A built-in reference genome is not available for the build associated with the selected input file".

 

Has anyone had this problem before.

Please help,

Le-Ann

ADD COMMENTlink modified 3.1 years ago by marcosp0 • written 4.1 years ago by mltlbrt10
1
gravatar for Jennifer Hillman Jackson
4.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Check the assigned "database" attribute for your files. GATK tools are locally pre-indexed for the human genome from 1000 genomes (hg_g1k_b37) on the public Main Galaxy instance http://usegalaxy.org.

To use another genome, follow the instructions for a custom reference genome:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

When using the tool form for this particular tool, the options to use a custom genome are:
Choose the source for the reference list: History
Using reference file: <the fasta dataset in your history for the genome>

Best, Jen, Galaxy team 

ADD COMMENTlink written 4.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for marcosp
3.1 years ago by
marcosp0
United States
marcosp0 wrote:

I have paired end reads of a trio that I eventually need to call variants on (make a .vcf). So I'm experiencing the same thing. Please tell me if my logic is correct:

FASTQ->FASTQC->BWA-MEM (Read group ID assigned as part of this step) -> Sort with SAM Tools -> Filter -> Clean ->Mark Duplicates -> Realign Indels (I think I have to import hg19 or b37 from Shared Data ->Data Libraries -> GATK -> hg19 (import to current history)).

Though I currently have it set to History under reference list, this message still comes upHistory does not include a dataset of the required format / build.There is also this section (Binding for reference-ordered data) which I'm not sure what to do with, I'm assuming setting it to indels.

Also, when moving processes forward, should it be the BAM-MEM files only for each step, or the descendent process (i.e. Sorted BAM to filtering  rather than the BAM-MEM). Please let me know if you need anymore information to answer my questions. This is a project due soon...

ADD COMMENTlink written 3.1 years ago by marcosp0

I posted this in the general forum, since it is a new question. 

ADD REPLYlink written 3.1 years ago by marcosp0
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 16.09
Traffic: 168 users visited in the last hour