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Question: Where to get SNPs and Indels?
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gravatar for PaulW
21 months ago by
PaulW • 60
PaulW • 60 wrote:

I downloaded some files from Broad Institute but Realigner Target Creator won't work with these files because the sort order is different to my BAM file.

/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf /hg19/dbsnp_138.hg19.excluding_sites_after_129.vcf /hg19/ucsc.hg19.fasta

I can't sort the BAM file to match these files because in Galaxy the REFERENCE parameter is hidden for the SortSAM tool.

Where can I get these files in the correct sort order?
realigner target creator • 627 views
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modified 21 months ago • written 21 months ago by PaulW • 60
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Assign the database "hg19" to the BAM datasets. This is how certain tools interpret the reference genome. I am assuming that you have installed this reference genome on your server already or it exists on the server you are working on.

Click on the pencil icon for the dataset to make the change. Next time, you can assign the database in the Upload tool if that is used.

Sorting help: https://github.com/jennaj/support-prior-qa/wiki/Sort-your-inputs

Note: GATK tools at http://usegalaxy.org are not natively indexed for hg19 and jobs run with a hg19 custom reference genome will often fail for memory. Instead, hg_g1k_v37 is the human build indexed (1000 Genomes version). Also - the tools here are deprecated and may not work - we will be hiding them soon so that they are not used. Most other tools (Samtools, Picard, Mapping and Variant analysis tools, etc) are indexed for hg19.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for PaulW
21 months ago by
PaulW • 60
PaulW • 60 wrote:

Thanks for your help. It turns out that Picard ReorderSAM allows sorting the BAM to match the reference file from Broad which then makes everything work fine :-)
ADD COMMENT • link written 21 months ago by PaulW • 60
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