Question: bam to VCF
gravatar for xlu1
11 months ago by
xlu120 wrote:


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 • 393 views
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by xlu120
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 ( 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 COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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