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Question: bam to VCF
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gravatar for xlu1
14 months ago by
xlu1 • 20
xlu1 • 20 wrote:

Hi,

I am trying to get all the variants from sequencing data. From fastaq, I got BAM files. Then I wanted to run Naive Variant Caller to get variants. Now the problem came, several times same error occurs "This job was terminated because it used more memory than it was allocated." Is there a different variant caller can use requiring less memory? Anybody can help? Thanks!
bowtie vcf bam • 522 views
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modified 14 months ago by Jennifer Hillman Jackson ♦ 25k • written 14 months ago by xlu1 • 20
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gravatar for Jennifer Hillman Jackson
14 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The data may really be too large to run with the Naive Variant Caller tool (with the current settings) or there could be a formatting problem triggering the error.

The NVC tool has several options to filter the data processed (region, read depth, base and map quality). Sorting the input BAM dataset can also help reduce memory usage during tool execution.

Also, consider double checking the upstream inputs and tool settings. Start by confirming the fastqsanger datatype/content is correct, the target genome used for mapping and NVC are correct (and the same), and that the custom reference genome (if one is used) is formatted correctly.

These Support FAQs cover how to troubleshoot tool/data issues (those mentioned above and others):

For examples of variant calling workflows, the Learn Galaxy tutorials can be reviewed:

If the NVC tool still fails after the checks, and you are working at Galaxy Main (https://usegalaxy.org) or can reproduce the issue there, a bug report can be sent in and we can help with troubleshooting. Please leave all datasets, inputs - outputs - plus any generated for troubleshooting, undeleted in the history and include a link to this post in the comments.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 14 months ago by Jennifer Hillman Jackson ♦ 25k
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