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.