Tagged with #validatesamfile
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I have a quick question about changes ReduceReads does to a file:

This is the output from a ValidateSamFile run before and after using ReduceReads on the latest nightly-build. Given that the best practices state that the SAM/BAM file must pass validation this is strange because it seems that ReduceReads is creating errors.

Any thoughts?

After: java -jar /usr/local/picard-tools/ValidateSamFile.jar I=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.reduced.bam IGNORE=MISSING_TAG_NM [Tue Nov 12 15:01:28 MST 2013] net.sf.picard.sam.ValidateSamFile INPUT=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.reduced.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Nov 12 15:01:28 MST 2013] Executing as srynearson@newrepublic.genetics.utah.edu on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_25-mockbuild_2013_06_26_07_26-b00; Picard version: 1.99(1563) ERROR: Record 20952, Read name 20524, Mate alignment does not match alignment start of mate ERROR: Record 490879, Read name 482367, Mate alignment does not match alignment start of mate ERROR: Record 514101, Read name 505228, Mate alignment does not match alignment start of mate ERROR: Record 863536, Read name 849794, Mate alignment does not match alignment start of mate ERROR: Record 1014607, Read name 998725, Mate alignment does not match alignment start of mate ERROR: Record 1025644, Read name 1009614, Mate alignment does not match alignment start of mate ERROR: Record 1121141, Read name 1103717, Mate alignment does not match alignment start of mate ERROR: Record 1248134, Read name 1228854, Mate alignment does not match alignment start of mate ERROR: Record 1278077, Read name 1258325, Mate alignment does not match alignment start of mate ERROR: Record 1301946, Read name 1281828, Mate alignment does not match alignment start of mate

Before: java -jar /usr/local/picard-tools/ValidateSamFile.jar I=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam IGNORE=MISSING_TAG_NM [Tue Nov 12 15:02:01 MST 2013] net.sf.picard.sam.ValidateSamFile INPUT=NA12761.mapped.ILLUMINA.bwa.CEU.exome.20121211.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Nov 12 15:02:01 MST 2013] Executing as srynearson@newrepublic.genetics.utah.edu on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_25-mockbuild_2013_06_26_07_26-b00; Picard version: 1.99(1563) INFO 2013-11-12 15:03:45 SamFileValidator Validated Read 10,000,000 records. Elapsed time: 00:01:43s. Time for last 10,000,000: 103s. Last read position: 2:74,687,627