search

BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
152 stars 49 forks source link

bedgraph coordinates bigger than chromosome length #65

Open gbdias opened 5 years ago

gbdias commented 5 years ago

Hi,

Currently FREEC outputs the copy numbers in bedGraph format. However, the last window on each chromosome usually extends past the actual chromosome length to maintain the fixed window size. This renders the file incompatible with the UCSC genome browser or UCSC conversion tools such as bedGraphToBigWig.

Although this can be fixed manually, it would be useful to have FREEC output UCSC-compatible bedGraph in the future.

Thanks