FreeBayes error when limit variant calling to a SNP region
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17 months ago
Kian ▴ 50

FreeBayes error when limit variant calling to a SNP region in RNASeq data

Input was the BAM file and the dataset of SNP that uploaded from UCSC to usegalaxy.

An error occurred with this dataset:
ERROR(freebayes): Invalid target region coordinates (chr13 58011599 58011599) right bound is lower than left bound!
ERROR(freebayes): Invalid target region coordinates (chr13 58012259 58012259) right bound is lower than left bound!


Anyone know whats the problem here?

tx

usegalaxy freebayes varinat calling SNP rnaseq • 506 views
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Yes, like the error message says, the right bound is lower than the left bound in those half-open intervals

A half-open interval includes only one of its endpoints, and is denoted by mixing the notations for open and closed intervals.[3] For example, (0,1] means greater than 0 and less than or equal to 1, while [0,1) means greater than or equal to 0 and less than 1