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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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amplicon data #22

Closed yiliu4234 closed 7 years ago

yiliu4234 commented 7 years ago

Hello I am trying to use FREE-C software for finding CNVs in amplicon sequencing data. I used pileup format as matefile ,both control and sample are pile up format , but I get error when it calculate BAF file

..use "pileup" format of reads to calculate BAF profiles ..Starting reading /home/ywliao/project/Gengyan/mpileup/pileup/spileup/wbcpileup/health1.pileup to calculate BAF profiles 段错误(吐核)

Please help me

valeu commented 7 years ago

Dear Yi Lui, Please send me your config and the complete output?

yiliu4234 commented 7 years ago

OK ! config_cervical.txt

![Uploading Screenshot from 2017-05-19 10-19-00.png…]() There are not files in Outputdir Thanks !

valeu commented 7 years ago

Dear Yi Lui, your config file seems OK to me. However, I need to see the complete output of FREEC into the command line.

yiliu4234 commented 7 years ago

This is output . stdout.txt Thanks very much !

valeu commented 7 years ago

It looks that you very few genes. In this case, you may consider using OncoCNV developed for amplicon-seq data.

If you want to run FREEC, I suggest that you exclude all chromosomes not present in your .bed file from the file with chromosome lengths.

yiliu4234 commented 7 years ago

Following your steps, I succeeded in running FREEC, thank you very much !