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Problem:

I have done:

cut -f FR07937945--FR07937944_gridss.vcf.gridss_RPostProcess.bedpe

and confirmed that all of the second column (QUAL) are digits. Some are integers, but most are floats.

Since line 387 of Event.java is:

int p1 = Integer.parseInt(bits[1]);

I guess there is an issue here.

Is it that BEDPE files shouldn't have floats in the QUAL col,
or is it that our file isn't a bedpe file, or is it that this is an error in clove?

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1 Answer

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Answer:

BED format

As described on the UCSC Genome see  below, 
the BED format is a concise and flexible way to represent genomic features and annotations. 
The BED format description supports up to 12 columns, but only the first 3 are required for the UCSC browser, 
the Galaxy browser and for bedtools. bedtools allows one to use the “BED12” format (that is, all 12 fields listed below). 
However, only intersectBed, coverageBed, genomeCoverageBed, and bamToBed will obey the BED12 “blocks” when computing overlaps, etc., 
via the “-split” option. For all other tools, the last six columns are not used for any comparisons by the bedtools. Instead, 
they will use the entire span (start to end) of the BED12 entry to perform any relevant feature comparisons. 
The last six columns will be reported in the output of all comparisons.

BEDPE format

We chose to define a new format because the existing “blocked” BED format (a.k.a. BED12)
 does not allow inter-chromosomal feature definitions. In addition, BED12 only has one strand field, 
which is insufficient for paired-end sequence alignments, especially when studying structural variation

GFF format  
Genome file format
SAM/BAM format
VCF format

 

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