Entering edit mode
8.4 years ago
morovatunc
▴
560
Hi
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.
Best regards,
T
Now people will complain my hours for " we cannot understand your output" please post understandable problems. thanks biostars for not letting my post my ls for 30 minutes.
Sorry for my bad england. I just had a bad day.