Variant Calling output problem GL000 contigs

Question

[morovatunc]

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

[morovatunc]

1 14 19 3 8 GL000194.1 GL000199.1 GL000204.1 GL000209.1 GL000214.1 GL000219.1 GL000224.1 GL000229.1 GL000234.1 GL000239.1 GL000244.1 GL000249.1 ICGC-effects-stats.genes.txt ICGC-files.list X 10 15 2 4 9 GL000195.1 GL000200.1 GL000205.1 GL000210.1 GL000215.1 GL000220.1 GL000225.1 GL000230.1 GL000235.1 GL000240.1 GL000245.1 ICGC-effects-filter-germline.vcf.gz ICGC-effects-stats.html ICGC.vcf.gz Y 11 16 20 5 GL000191.1 GL000196.1 GL000201.1 GL000206.1 GL000211.1 GL000216.1 GL000221.1 GL000226.1 GL000231.1 GL000236.1 GL000241.1 GL000246.1 ICGC-effects-filter-germline.vcf.gz.tbi ICGC-effects-stats.yaml ICGC.vcf.gz.tbi 12 17 21 6 GL000192.1 GL000197.1 GL000202.1 GL000207.1 GL000212.1 GL000217.1 GL000222.1 GL000227.1 GL000232.1 GL000237.1 GL000242.1 GL000247.1 ICGC-effects-filter.vcf.gz ICGC-effects.vcf.gz MT 13 18 22 7 GL000193.1 GL000198.1 GL000203.1 GL000208.1 GL000213.1 GL000218.1 GL000223.1 GL000228.1 GL000233.1 GL000238.1 GL000243.1 GL000248.1 ICGC-effects-filter.vcf.gz.tbi ICGC-effects.vcf.gz.tbi tx

[morovatunc]

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.