Hi, 

I have two bam files from ICGC. During mutation calling, vardict/mutect/freebayes/varscan split bam to by its chromosomes. Those GL00 parts also appear just like chr1-2-3-4-5-6-7 appear. I check what they are and found they are contigs?!?(forgive my ignorance) How should I treat them ? Will they cause a problem during variant calling output interpretation? I read one previous thread about this but there were not any information about how to treat them. I need your help.

Best,

Tunc.
You can check http://genome.ucsc.edu/cgi-bin/hgGateway where they provide details for every assembly.

This was addressed on the UCSC genome support forum:
http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=8701&S=5061c99adf3f4c4ee90f0ea362d838c7

> chr*_random - are called "unlocalized" sequences. The chromosome is
> known, but not the location on the chromosome. chrUn_* - are called
> "unplaced" sequences. They probably belong to the sequenced genome,
> but placement is unknown at this time.
> The GL numbers (or other types of numbers) in these names are the
> genbank identification numbers which can be used in a nucleotide
> search at Entrez. For example: chr1_GL456211_random - unlocalized
> sequence belonging to chr1, NCBI identification: GL456211
> chrUn_JH584304 - unplaced sequence, NCBI identification JH584304