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GATK filters the majority of reads

AmirAmir Member
edited August 2012 in Ask the GATK team

I'm using GATK to call the variants from a bam file. However, it seems that GATK filters out 70% of the reads. I've checked the phred score of the reads and found out that many reads have a score of 255 which means that the phred score is not available for that given read. I'm afraid this has made the problem. I would appreciate if somebody can help me fix this issue. It is really urgent for me since I need to process these data as soon as possible. Here is the output i get from GATK:

17:33:35,415 TraversalEngine - Total runtime 110033.08 secs, 1833.88 min, 30.56 hours
17:33:35,427 TraversalEngine - 216725269 reads were filtered out during traversal out of 301944869 total (71.78%)
17:33:35,428 TraversalEngine - -> 11269126 reads (3.73% of total) failing DuplicateReadFilter
17:33:35,428 TraversalEngine - -> 205456143 reads (68.04% of total) failing MappingQualityUnavailableFilter
17:34:11,424 RestStorageService - Error Response: PUT '/GATK_Run_Reports/dRmHhXABKsxRPkAlvOQ2fIMA5kAeWHVA.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Fo
en, Request Headers: [Content-Length: 342, Content-MD5: fsArqc4sL6RGGDVR1rWMdQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 7ec02ba9ce2c2fa4461
d6b58c75, Date: Fri, 10 Aug 2012 00:34:06 GMT, Authorization: AWS AKIAJXU7VIHBPDW4TDSQ:J4sgp1xD1b1TCfpN4XDr6HJxVDk=, User-Agent: JetS3t/0.8.1 (Windows 7/6.1; amd6
; JVM 1.7.0_04), Host: s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 2085AF3BB535FEEE, x-amz-id-2: 2EQ7Wp7M9v6Xa59jfLmxF9q6Ew55he9
rMVz6HX4Aml8Hi407ULgwkgTb0bA, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 09 Aug 2012 21:34:27 GMT, nnCoection: close, Server: AmazonS3]

17:34:11,783 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximate
0783 seconds. Retrying connection.


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