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cauyrd / ScanIndel

The integrated pipeline for Indel detection
GNU General Public License v3.0
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Variants are called outside the specified bed file #9

Open erfan1985 opened 6 years ago

erfan1985 commented 6 years ago

I set the -t parameter to limit the variant calls to bed file containing the regions of interest. However, freebayes still calls variants outside the regions. The bed file is fine and it seems like the called variants are near my specified regions and none happening in chromosomes not listed in the bed file.

Is this because the variants will be called as long as the reads overlap the regions?

I have to re-filter using bcftools at the end. Is there any solution to force limit the calls to the bed regions during the operation? I imagine that would save time.

erfan1985 commented 6 years ago

After a while coming back to this I think I figured it out myself. The script has to be modified and where the Freebayes is called, it should be specified that we are interested only in the regions listed in the bed file. So all I did was to add ' -t '+bedfile+ to line 450 just after reference['freebayes'], Seems like this solved the issue.

Cheers