Question: Realigner Target Creator in GATKtools
1
gravatar for mltlbrt
4.0 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 3.0 years ago by marcosp0 • written 4.0 years ago by mltlbrt10
1
gravatar for Jennifer Hillman Jackson
4.0 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 4.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for marcosp
3.0 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 3.0 years ago by marcosp0

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

ADD REPLYlink written 3.0 years ago by marcosp0
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