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Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF
Apache License 2.0
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error in mainifest #23

Closed dora201888 closed 6 years ago

dora201888 commented 6 years ago

When I run gtc_to_vcf.py on my OmniX data, I got some errors as follows,

2018-09-12 15:17:32,991 - GTC converter - INFO - Processing 1 GTC files 2018-09-12 15:17:32,992 - GTC converter - INFO - Caching reference data 2018-09-12 15:18:11,128 - GTC converter - INFO - Finished caching reference data 2018-09-12 15:18:11,129 - GTC converter - INFO - Handling GTC file /gpfs/gsfs3/users/guow4/projectX1_2018/NIMHfamily/data/201805230017_R01C01.gtc 2018-09-12 15:18:11,166 - GTC converter - WARNING - Provided manifest name: /data/guow4/projectX1_2018/NIMHfamily/GP0441-IN1_NCIprocessed/GP0441-IN1_AnalysisManifest_2918.csv and manifest file used to generate GTC file: InfiniumOmniExpress-24v1-2_A1.bpm do not match, skipping

manifest.csv file> Sample_ID SentrixBarcode_A SentrixPosition_A Sample_Plate Sample_Well Sample_Group Gender Sample_Name
SC103044_PC04743_A01 2.02E+11 R01C01 WG4001934-DNA A01 sAASP-001 M 1760018
SC102980_PC04743_B01 2.02E+11 R03C01 WG4001934-DNA B01 sAASP-001 F 1866001

Could somebody help me to figure out if the error is due to wrong manifest file or not? I am new to this field. Thanks.

KelleyRyanM commented 6 years ago

Hi, In this case, it looks like a sample sheet has been provided as input, rather than a manifest. This manifest is available for download from ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/productfiles/humanomniexpress-24/v1-2/infinium-omniexpress-24-v1-2-a1-manifest-file-csv.zip (would need to be unzipped before providing as input). -Ryan