This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
GATK filters the majority of reads
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.