I am using bcbio to call variants of tumor-normal cancer paired data. I am using icgc data so I am pretty sure about the quality of the data. In bcbio, i specify the genome assebly as it is grch37. However, I obtained this "GLL00.." files as it called all the mutations by chromosome. I looked at the definition about what these may be ? but as far as learned that these are the contigs in the chromosomes.
Please forgive my ignorance in this subject. Also, I will have around ~200 samples like this so, should I preprocess my data to get rid of these contigs?
Thank you for your info.